Package required but not available: 'Rcpp'

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

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

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

Packages suggested but not available for checking: 'ICS', 'ICSNP'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'digest', 'fst', 'posterior', 'purrr', 'qs', 'R2jags',
  'rjags', 'rlang', 'targets', 'tarchetypes', 'tibble', 'withr'

Packages suggested but not available for checking:
  'dplyr', 'fs', 'knitr', 'R.utils', 'rmarkdown', 'testthat', 'tidyr',
  'visNetwork'

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

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

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

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: 'rjson', 'naturalsort'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
Note: found 1 marked UTF-8 string
Running examples in 'janeaustenr-Ex.R' failed
The error most likely occurred in:

> ### Name: austen_books
> ### Title: Tidy data frame of Jane Austen's 6 completed, published novels
> ### Aliases: austen_books
> 
> ### ** Examples
> 
> 
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Running 'testthat.R'
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', 'lifecycle', 'lubridate', 'magrittr', 'purrr', 'rlang',
  'stringi', 'stringr', 'snakecase', 'tidyselect', 'tidyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jsonlite', 'crul', '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:
  'dplyr', 'geosphere', 'lifecycle', 'magrittr', 'purrr', 'rlang',
  'sf', 'stringr', 'tibble', 'tidyr', 'units', '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:
  'cli', 'dplyr', 'httr', 'pillar', 'progress', 'purrr', 'rlang',
  'stringi', 'stringr', 'tibble', 'tidyr', 'vctrs'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjags', 'R2jags', 'tidyverse', 'tidyr', 'ggplot2', 'ggExtra',
  'gridExtra', 'mcmcplots'

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: 'rJava'

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

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

VignetteBuilder 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', 'reactR', 'stringr', 'magrittr', 'readr',
  'jsonlite', 'httpuv', 'mime', 'cli', 'ids', '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:
  'stringr', 'RColorBrewer', 'maps', 'rworldmap', 'ggplot2', 'sp'

Package suggested but not available for checking: 'ncdf4'

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

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

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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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: 'bookdown', 'rmarkdown'

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

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',
  'philentropy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'renv', 'remotes', 'desc', 'docopt'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xts', 'fPortfolio', 'caret', 'magrittr', 'tcltk2', 'zoo'

Packages suggested but not available for checking:
  'BurStFin', 'data.table', 'DescTools', 'fAssets', 'fBasics',
  'forecast', 'FRAPO', 'h2o', 'iClick', 'keras', 'quantmod', 'rugarch',
  'tensorflow', 'tibble', 'timeDate', 'timeSeries', 'timetk'

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

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

VignetteBuilder packages required for checking but not installed:
  'knitr', 'ggplot2', 'RColorBrewer'

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

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

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

Package suggested but not available for checking: 'XLConnect'

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ellipse', 'mvtnorm', 'expm', 'matrixcalc', 'lvm4net', 'pROC',
  'network'

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

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

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

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

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: 'VGAM', 'statmod'

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 suggested but not available for checking: 'testthat'
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
JBTest: no visible global function definition for 'pchisq'
generateSignificance: no visible global function definition for 'pnorm'
packages: no visible global function definition for 'install.packages'
shift: no visible global function definition for 'tail'
shift: no visible global function definition for 'head'
splitBy: no visible global function definition for 'head'
Undefined global functions or variables:
  head install.packages pchisq pnorm tail
Consider adding
  importFrom("stats", "pchisq", "pnorm")
  importFrom("utils", "head", "install.packages", "tail")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'xtable'
Packages suggested but not available for checking:
  'agricolae', 'coin', 'fastGraph'
Packages unavailable to check Rd xrefs: 'coin', 'fastGraph', 'agricolae'
Packages required but not available:
  'jmvcore', 'evaluate', 'rappdirs', 'httr', 'Rcpp', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'rlang', 'jsonlite', 'base64enc', 'stringi'

Packages suggested but not available for checking:
  'testthat', 'RProtoBuf', 'knitr', 'ggplot2', 'RColorBrewer', 'ragg',
  'fastmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jmvcore', 'R6', 'car', 'multcomp', 'ggplot2', 'PMCMR', 'emmeans',
  'vcd', 'vcdExtra', 'GGally', 'BayesFactor', 'psych', 'GPArotation',
  'afex', 'mvnormtest', 'lavaan', 'ggridges', 'ROCR'

Packages suggested but not available for checking:
  'exact2x2', 'testthat', 'semPlot', 'carData', 'knitr', 'rmarkdown'

VignetteBuilder 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', 'zip'

Packages suggested but not available for checking:
  'jmv', 'jmvcore', 'haven', 'knitr', 'rmarkdown', 'RProtoBuf',
  '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: 'rstudioapi', 'digest'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'mvtnorm'

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

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
RE.ADT: no visible global function definition for 'sd'
RE.ADT: no visible global function definition for 'pnorm'
RE.Johnson: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm sd
Consider adding
  importFrom("stats", "pnorm", "sd")
to your NAMESPACE file.
Packages required but not available:
  'cobs', 'doParallel', 'foreach', 'generics', 'ggplot2', 'lme4',
  'mvtnorm', 'randtoolbox', 'Rcpp', 'tibble', 'RcppArmadillo'

Packages suggested but not available for checking:
  'bindrcpp', 'dplyr', 'JM', 'joineR', '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: 'statmod'

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: 'glmnet', 'palasso', 'cornet'

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

Packages which this enhances but not available for checking:
  'mice', 'earth', 'spls', 'MRCE', 'remMap',
  'MultivariateRandomForest', 'SiER', 'mcen', 'GPM', 'RMTL', 'MTPS'

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

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

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

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

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

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: 'lme4', 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lpSolve', 'pcaPP', 'igraph', 'JGL', 'brainR', 'misc3d', 'oro.nifti',
  'shiny', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
binteg: no visible global function definition for 'contourLines'
binteg: no visible global function definition for 'approx'
binteg: no visible global function definition for 'par'
plot1: no visible global function definition for 'par'
plot1: no visible global function definition for 'rect'
plot1: no visible global function definition for 'axis'
plot1: no visible global function definition for 'contour'
plot1: no visible global function definition for 'contourLines'
plot1: no visible binding for global variable 'approx'
plot1: no visible global function definition for 'lines'
plot1: no visible global function definition for 'text'
plot2: no visible global function definition for 'abline'
plot2: no visible global function definition for 'lines'
plot2: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par rect text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
Packages required but not available: 'acnr', 'matrixStats', 'DNAcopy'

Packages suggested but not available for checking:
  'PSCBS', 'R.cache', 'digest', 'changepoint', '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:
  'readxl', 'openxlsx', 'timeSeries', 'data.table', 'rChoiceDialogs',
  'R.utils', 'rJava', 'Rcpp', 'timeDate'

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

VignetteBuilder 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', 'ordinal', 'tibble'

Package suggested but not available for checking: 'mitml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'SpATS', 'colorspace', 'fds', 'ggplot2', 'fields', 'spam', 'SemiPar'

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

Packages suggested but not available 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: 'xtable'
Errors in running code in vignettes:
when running code in 'JoSAE.Rnw'

> library(JoSAE)
Loading required package: nlme

> data(JoSAE.domain.data)

> data(JoSAE.sample.data)

> library(lattice)

> print(xyplot(biomass.ha ~ mean.canopy.ht | domain.ID, 
+     data = JoSAE.sample.data))

> summary(fit.lme <- lme(biomass.ha ~ mean.canopy.ht, 
+     data = JoSAE.sample.data, random = ~1 | domain.ID))
Linear mixed-effects model fit by REML
  Data: JoSAE.sample.data 
       AIC      BIC    logLik
  1553.764 1565.616 -772.8822

Random effects:
 Formula: ~1 | domain.ID
        (Intercept) Residual
StdDev:    10.30361 49.85829

Fixed effects:  biomass.ha ~ mean.canopy.ht 
                  Value Std.Error  DF   t-value p-value
(Intercept)    6.694678  8.334032 130  0.803294  0.4233
mean.canopy.ht 1.375782  0.077531 130 17.744832  0.0000
 Correlation: 
               (Intr)
mean.canopy.ht -0.754

Standardized Within-Group Residuals:
        Min          Q1         Med          Q3         Max 
-3.12149463 -0.56323615 -0.05238025  0.55696863  3.11427777 

Number of Observations: 145
Number of Groups: 14 

> d.data <- JoSAE.domain.data

> names(d.data)[3] <- "mean.canopy.ht"

> result <- eblup.mse.f.wrap(domain.data = d.data, lme.obj = fit.lme)

> library(xtable)

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

  'JoSAE.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
--- re-building 'JoSAE.Rnw' using Sweave
Loading required package: nlme

Error: processing vignette 'JoSAE.Rnw' failed with diagnostics:
 chunk 8 
Error in library(xtable) : there is no package called 'xtable'

--- failed re-building 'JoSAE.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'utf8', 'magrittr'

Package suggested but not available for checking: 'covr'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'stringi', 'dplyr', 'purrr', 'tibble', 'rlang', 'httr',
  'shiny', 'rmarkdown', 'knitr'

Packages suggested but not available for checking:
  'testthat', 'data.table', 'tidyr', 'rclipboard', 'tinytex', 'DT'

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'leaflet', 'memoise', 'miniUI', 'purrr', 'rlang', 'sf', 'shiny',
  'tibble', 'units', 'magrittr', 'vctrs'

Packages suggested but not available for checking:
  'knitr', 'lintr', 'lwgeom', 'testthat', 'rmarkdown', '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:
  'dplyr', 'httr', 'pillar', 'progress', 'purrr', 'rlang', 'stringi',
  'stringr', 'tibble', 'tidyr', 'vctrs', 'lubridate', 'navigatr'

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

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

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

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httpuv', 'jsonlite', 'stringr', 'stringi', 'mime', 'R6', 'R.utils'

Package suggested but not available for checking: 'testthat'

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

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

Packages suggested but not available 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', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'V8', 'rstudioapi'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'coda', 'corrplot', 'stringi', 'doParallel', 'foreach',
  'RcppArmadillo', 'RcppGSL'

Packages suggested but not available for checking:
  'knitr', 'kableExtra', 'raster', 'sp', 'rgdal', 'dplyr', 'rmarkdown',
  'bookdown', 'testthat', 'boral', 'Hmsc', 'BayesComm', 'snow',
  'snowfall', 'ggplot2'

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

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

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

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

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

Packages suggested but not available for checking:
  'covr', 'lavaan', 'markdown', 'mediation', 'patchwork',
  'performance', 'processR', 'rmarkdown', 'roxygen2', 'see', 'stringr',
  '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:
  'data.table', 'shiny', 'readxl', 'DT', 'jstable', 'labelled',
  'GGally', 'ggplot2', 'haven', 'rstudioapi', 'shinycustomloader',
  'MatchIt', 'survey', 'jskm', 'purrr', 'geepack', 'maxstat', 'survC1',
  'survIDINRI', 'timeROC', 'shinyWidgets', 'pROC', 'Hmisc', 'see',
  'readr', 'RColorBrewer', 'ggpubr', 'officer', 'rvg', 'devEMF',
  'epiDisplay'

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

VignetteBuilder 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'

Package suggested but not available for checking: 'testthat'

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

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

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

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: 'V8', 'jsonlite', 'curl'

Package suggested but not available for checking: 'spelling'

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

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'
Package unavailable to check Rd xrefs: 'vctrs'
Running examples in 'jsonlite-Ex.R' failed
The error most likely occurred in:

> ### Name: rbind_pages
> ### Title: Combine pages into a single data frame
> ### Aliases: rbind_pages
> 
> ### ** Examples
> 
> # Basic example
> x <- data.frame(foo = rnorm(3), bar = c(TRUE, FALSE, TRUE))
> y <- data.frame(foo = rnorm(2), col = c("blue", "red"))
> rbind_pages(list(x, y))
Error: Required package vctrs not found. Please run: install.packages('vctrs')
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #This file runs all unit tests on every R CMD check.
  > #Comment this out to disable.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'cli', 'dplyr', 'jsonlite', 'rlang'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bit64', 'DBI', 'glue', 'jsonlite', 'magrittr', 'pillar', 'purrr',
  'rlang', 'RSQLite', 'tibble', 'tidyselect', 'vctrs', 'withr'

Packages suggested but not available for checking:
  'curl', 'dplyr', 'knitr', 'repurrrsive', '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: 'V8'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'V8'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geepack', 'lme4', 'data.table', 'labelled', 'tableone', 'coxme',
  'survey', 'dplyr', 'purrr', 'magrittr', 'tibble'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'purrr', 'xml2', 'magrittr', 'stringr', 'readr',
  'tibble', 'rlang', 'furrr', 'pryr', 'crayon', 'cli'

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

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

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

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:
  'htmlwidgets', 'shiny', 'htmltools', 'rstudioapi', 'shinyAce',
  'miniUI', 'base64enc', 'R.utils', 'fontawesome', 'jquerylib'

Packages suggested but not available for checking: 'jsonlite', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'igraph', 'sparta', '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:
  'crayon', 'generics', 'ggplot2', 'magrittr', 'pander', 'pkgconfig',
  'rlang', 'tibble'

Packages suggested but not available for checking:
  'broom', 'broom.mixed', 'ggstance', 'huxtable', 'kableExtra', 'lme4',
  'lmerTest', 'pbkrtest', 'RColorBrewer', 'sandwich', 'scales',
  'survey', 'weights', 'knitr', 'rmarkdown', 'testthat'

Packages which this enhances but not available for checking:
  'brms', 'quantreg', 'rstanarm'

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: 'nortest', 'knitr'
qtls: no visible global function definition for 'quantile'
qtls: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm quantile
Consider adding
  importFrom("stats", "pnorm", "quantile")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'nortest'
Packages required but not available:
  'yaml', 'xts', 'zoo', 'readxl', 'data.table', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'tinytex', 'R.rsp', 'testthat', 'roxygen2', 'scales',
  'shape'

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: 'XML', 'RCurl'

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

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

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

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

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', 'future'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'magrittr', 'dplyr', 'purrr', 'pdftools', 'rvest', 'stringr',
  'SwimmeR', '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: 'Rcpp', 'RcppEigen'

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

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

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

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'knitr', 'magrittr', '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:
  'data.tree', 'DiagrammeR', 'DiagrammeRsvg', 'purrr', 'yaml', 'yum'

Packages suggested but not available for checking:
  'covr', 'here', 'jsonlite', '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:
  'BayesFactor', 'ggplot2', 'stringr', 'shiny', 'Superpower', 'pwr',
  'shinydashboard', 'qpdf'

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: 'remotes', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'box', '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:
  'multcompView', 'emmeans', 'data.table', 'ggthemes', 'ggplot2',
  'ggpubr', 'mice', 'psych', 'rms', 'robustbase', 'quantreg', 'lavaan',
  'VGAM', 'lme4', 'extraoperators'

Packages suggested but not available for checking:
  'scales', 'foreach', 'testthat', 'covr', 'knitr', 'rmarkdown',
  'pander', 'GPArotation'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'magrittr', 'stringr', 'xml2', 'rvest', 'rmarkdown',
  'scales', 'viridisLite', 'htmltools', 'rstudioapi', 'glue',
  'webshot', 'digest', 'svglite'

Packages suggested but not available for checking:
  'testthat', 'magick', 'formattable', 'sparkline'

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:
  'arkhe', 'dimensio', 'extraDistr', 'ggplot2', 'Hmisc', 'rlang'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigmemory', 'sqldf', 'biomaRt', 'KEGGgraph', 'CompQuadForm',
  'data.table', 'igraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rcdd', 'gmp', 'lpSolve', 'Rglpk', 'slam', 'CVXR'

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: 'affy', 'Biobase'

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

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

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

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

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

Package suggested but not available for checking: 'locfit'

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

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

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:
  'circular', 'MVN', 'tcltk2', 'tseriesChaos', 'stlplus', 'tseries',
  'forecast', 'stinepack', 'missForest', 'nonlinearTseries', 'zoo',
  'rgl', 'infotheo', 'plot3D'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'V8'

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

VignetteBuilder 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', 'forcats', 'dplyr', 'tidyr', 'stringr',
  'scales'

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

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

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

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

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:
  'RColorBrewer', 'roll', 'foreach', 'doParallel', 'Rcpp'

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

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

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

Packages suggested but not available for checking:
  'R.rsp', 'VineCopula', '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: 'assertthat', 'univariateML', 'EQL'

Packages suggested but not available for checking:
  'extraDistr', 'SkewHyperbolic', '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: 'ape', 'distory', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'qrng', 'cctools', 'kdecopula', 'VineCopula', 'doParallel',
  'foreach'

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
Package required but not available: 'checkmate'

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', 'covr', 'ggplot2',
  'tidytext', 'printr', 'scales', 'BH', 'sf'

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: 'nor1mix', 'ks', 'sm', 'locfit', 'orthopolynom'
Package suggested but not available for checking: 'Oarray'
Package unavailable to check Rd xrefs: 'Oarray'
Packages required but not available:
  'Hmisc', 'raster', 'reshape2', 'stringr', 'sp', 'xts', 'zoo'

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

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', 'dplyr', 'tibble', 'actuar'

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: 'lme4', 'metafor'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'generics', 'reticulate', 'tensorflow', 'tfruns', 'magrittr',
  'zeallot', 'glue', 'R6', 'ellipsis', 'rlang'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'knitr', 'rmarkdown', 'callr', 'tfdatasets',
  'withr', 'jpeg'

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

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

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:
  'reticulate', 'tensorflow', 'rstudioapi', 'plotly', 'data.table',
  'RJSONIO', 'rjson', 'tidyjson', 'dplyr', 'echarts4r', 'crayon',
  'keras', 'magick'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'testthat', 'nloptr', 'numDeriv', 'doParallel', 'doFuture'

Packages suggested but not available for checking:
  'DiceKriging', 'DiceDesign', 'inline', 'foreach', 'knitr', 'ggplot2',
  'reshape2', 'corrplot'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ks', 'sparr', 'sp', 'plyr', 'dplyr', 'fastmatch', 'fitdistrplus',
  'GB2', 'magrittr', 'mvtnorm'

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

Packages suggested but not available for checking:
  '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:
  'benchmarkme', 'directlabels', 'dplyr', 'ggplot2', 'gridExtra',
  'Hmisc', 'pbapply', 'rgdal', 'reshape2', 'wordspace'

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

Packages suggested but not available for checking:
  'bindata', '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: 'rgl', 'foreach', 'doParallel', 'GA'

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

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

Packages suggested but not available for checking: 'gdata', 'org.Hs.eg.db'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'carData'
Packages required but not available:
  'shinyBS', 'shiny', 'htmltools', 'config', 'data.table', 'dplyr',
  'DT', 'ggplot2', 'golem', 'plotly', 'reactable', 'rintrojs', 'rlang',
  'shinycssloaders', 'shinydashboard', 'shinydashboardPlus',
  'shinyhelper', 'shinyWidgets', 'stringr', 'visNetwork', 'yaml'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'fastmap', 'future.apply', 'ggplot2', 'ggrepel',
  'magrittr', 'matrixNormal', 'pgdraw', 'purrr', 'quanteda', 'rlang',
  'stringr', 'tibble', 'tidyr', 'RcppEigen', 'RcppProgress'

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

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

Package suggested but not available for checking: 'epade'

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', 'rlang', 'tibble'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'askpass', 'openssl', 'R6', 'sodium', 'yaml',
  'filelock', 'rappdirs'

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'openssl', 'stringr', '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:
  'caret', 'doParallel', 'flextable', 'foreach', 'GPArotation',
  'knitr', 'lavaan', 'officer', 'rmarkdown', 'semPlot', 'semTools',
  'simstandard'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'lme4', 'testthat'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/KFAS.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/KFAS.Rnw'
(Is a VignetteBuilder field missing?)
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'kernlab'

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

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

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:
  'dlm', 'dse', 'FKF', 'KFAS', 'numDeriv', 'stsm'
Package unavailable to check Rd xrefs: 'stsm'
Running examples in 'KFKSDS-Ex.R' failed
The error most likely occurred in:

> ### Name: DS
> ### Title: Disturbance Smoother for State Space Models
> ### Aliases: DS DS.deriv
> ### Keywords: ts, model
> 
> ### ** Examples
> 
> # local level plus seasonal model with arbitrary parameter values
> # for the 'JohnsonJohnson' time series
> m <- stsm::stsm.model(model = "llm+seas", y = JohnsonJohnson, 
+   pars = c("var1" = 2, "var2" = 15, "var3" = 30))
Error in loadNamespace(x) : there is no package called 'stsm'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'kader', 'pracma', 'fdapace', 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'shinythemes', '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: 'R6', 'pracma', 'pspline', 'mvtnorm'

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

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:
  'abind', 'deepnet', 'ggplot2', 'gridExtra', 'magrittr',
  'matrixStats', 'png', 'shiny', 'stringr'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'crayon', 'fansi', 'ggplot2', 'ggraph', 'knitr', 'rmarkdown',
  'scales', 'spacesXYZ', 'testthat', 'vdiffr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'spacesXYZ', 'ggplot2'
Running examples in 'khroma-Ex.R' failed
The error most likely occurred in:

> ### Name: compare
> ### Title: Colour Difference
> ### Aliases: compare
> 
> ### ** Examples
> 
> # Trichromat
> pal <- colour("bright")
> 
> (deltaE <- compare(pal(5)))
Error: Package spacesXYZ 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
Packages required but not available:
  'R6', 'data.table', 'stringr', 'purrr', 'jsonlite', 'rio', 'tibble',
  'dplyr', 'magrittr', 'tidyr', 'elastic', 'Biostrings', 'Rsamtools',
  'rtracklayer'

Packages suggested but not available for checking:
  'ggplot2', 'readr', 'xml2', 'yaml', 'testthat', 'rmarkdown', 'knitr'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'memoise', 'plyr', 'pryr'

Package suggested but not available for checking: 'testthat'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'readr', 'shiny', 'shinythemes', 'ggrepel',
  'fitdistrplus', 'LaplacesDemon', 'here', 'tibble', 'magrittr',
  'plotly', 'dplyr', 'rlang', 'tidyselect', 'stringr'

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

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'markdown', '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:
  'circular', 'lqmm', 'splancs', 'sp', 'plotrix'

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

Package suggested but not available for checking: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'git2r'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kirby21.base'

Package suggested but not available for checking: 'kirby21.t1'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kirby21.base'

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

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

Packages suggested but not available for checking:
  'dplyr', 'tibble', 'RColorBrewer', 'signal', 'testthat', 'knitr',
  'rmarkdown', 'formatR', 'covr'

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

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

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

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

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:
  'grpreg', 'knockoff', 'doParallel', 'foreach', 'ExtDist'

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

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

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

Packages suggested but not available for checking:
  'scatterplot3d', 'som', 'mlbench', 'e1071'

Packages which this enhances but not available for checking:
  'clustMixType', 'randomForest', 'ClustVarLV'

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

Package suggested but not available for checking: 'testthat'

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

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

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

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

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: 'coca', 'RColorBrewer', 'pheatmap'

Packages suggested but not available for checking:
  'Rmosek', 'tikzDevice', 'mclust', '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:
  'blink', 'plyr', 'Rcpp', 'stringi', 'SnowballC'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
comp.npci: no visible global function definition for 'qnorm'
epband.fun: no visible global function definition for 'data'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible global function definition for 'data'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
lrt.confints: no visible global function definition for 'qchisq'
rothman.fun: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Packages required but not available: 'rootSolve', 'emplik', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dscore: no visible global function definition for 'glm'
dscore: no visible binding for global variable 'binomial'
dscore: no visible global function definition for 'pnorm'
pearson.group: no visible global function definition for 'cor'
spearman.group: no visible global function definition for 'cor'
sscore: no visible global function definition for 'glm'
sscore: no visible binding for global variable 'binomial'
sscore: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binomial cor glm pnorm
Consider adding
  importFrom("stats", "binomial", "cor", "glm", "pnorm")
to your NAMESPACE file.
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: 'openssl', 'phylogram', 'Rcpp'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clv', 'rgl', 'misc3d', 'longitudinalData', 'kml'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
C_zero : <anonymous>: no visible global function definition for 'runif'
get_extra_centroid_index: no visible global function definition for
  'head'
get_within_cluster_ss: no visible global function definition for
  'aggregate'
kmod: no visible global function definition for 'head'
kmod: no visible global function definition for 'tail'
Undefined global functions or variables:
  aggregate head runif tail
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'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:
  'checkmate', 'cowplot', 'ggplot2', 'pammtools', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'covr', 'devtools', 'knitr', 'rmarkdown', 'simsurv',
  'testthat', '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: 'lpSolve'

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

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: 'RefManageR', 'digest', '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.
Package required but not available: '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: 'knitr', 'rmarkdown', 'markdown'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'corrplot', 'ggplot2', 'igraph', 'maps',
  'mapproj', 'maptools', 'plyr', 'reshape2', '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: 'knitr', 'xfun'

Packages suggested but not available for checking:
  'gpg', 'rmarkdown', 'magrittr', 'shiny', 'miniUI', 'rstudioapi',
  'DT', 'digest'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'purrr', 'testthat', 'covr', 'mockr', '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:
  'evaluate', 'highr', 'stringr', 'yaml', 'xfun'

Packages suggested but not available for checking:
  'markdown', 'formatR', 'testit', 'digest', 'rgl', 'rmarkdown',
  'htmlwidgets', 'webshot', 'tikzDevice', 'tinytex', 'reticulate',
  'JuliaCall', 'magick', 'png', 'jpeg', 'gifski', 'xml2', 'httr',
  'DBI', 'showtext', 'tibble', 'sass', 'bslib', 'ragg', 'styler',
  'targets'

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', 'FNN'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'rbeta'
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'runif'
calculate.power : <anonymous>: no visible binding for global variable
  'quantile'
generate.benchmark.data: no visible global function definition for
  'runif'
generate.benchmark.data: no visible global function definition for
  'rnorm'
generate.benchmark.data: no visible global function definition for
  'rbinom'
generate.patchwork.copula: no visible global function definition for
  'rbeta'
generate.patchwork.copula: no visible global function definition for
  'runif'
novelTest.chisq: no visible global function definition for 'pchisq'
novelTest.chisq4nn: no visible global function definition for 'pchisq'
optimise.copula.mi : <anonymous>: no visible global function definition
  for 'optimize'
power.plot: no visible global function definition for 'axis'
power.plot : <anonymous>: no visible global function definition for
  'points'
power.plot: no visible global function definition for 'legend'
roc.plot: no visible global function definition for 'colorRampPalette'
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for 'points'
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for 'runif'
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq points quantile rbeta
  rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available:
  'parallelDist', 'forecast', 'doParallel', 'foreach', 'plyr'

Packages suggested but not available for checking: 'tseries', 'tsibble'

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

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:
  'Rdsdp', 'corpcor', 'glmnet', 'RSpectra', 'gtools'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'lars', 'ranger', 'stabs',
  'RPtests', '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:
  'seqminer', 'bigmemory', 'CompQuadForm', 'data.table', 'SPAtest',
  'irlba'

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

Packages suggested but not available for checking:
  'raster', 'rgbif', 'VARSEDIG'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'dplyr', 'httr', 'jsonlite', 'lubridate', 'purrr',
  'rlang', 'rstudioapi', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

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

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

Package suggested but not available for checking: 'testthat'

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

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

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:
  'glue', 'rlang', 'sf', 'stringr', 'tibble'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'knitr'

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

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

Packages suggested but not available for checking:
  'margins', 'pbkrtest', 'devtools', 'forcats', 'knitr', 'lme4',
  'rmarkdown', 'roxygen2', 'testthat', 'ggrepel', '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'

Package suggested but not available for checking: 'testthat'

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

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

Packages suggested but not available for checking:
  'testthat', 'tm', 'SnowballC', 'shiny', 'knitr', 'rmarkdown',
  'koRpus.lang.de', 'koRpus.lang.en', 'koRpus.lang.es',
  'koRpus.lang.fr', 'koRpus.lang.it', 'koRpus.lang.nl',
  'koRpus.lang.pt', 'koRpus.lang.ru'

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

VignetteBuilder 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', 'ordinalNet'

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

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:
  'pcalg', 'energy', 'kernlab', 'RSpectra', 'graph'

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

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

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

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', '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 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: 'Rcpp', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'maps'
Malformed Description field: should contain one or more complete sentences.
image.kriging: no visible global function definition for 'heat.colors'
image.kriging: no visible global function definition for 'image'
kriging: no visible global function definition for 'lm'
plot.kriging: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve heat.colors image lm
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image")
  importFrom("stats", "lm")
to your NAMESPACE file.
Running examples in 'kriging-Ex.R' failed
The error most likely occurred in:

> ### Name: kriging
> ### Title: Ordinary Kriging
> ### Aliases: kriging
> ### Keywords: datagen models
> 
> ### ** Examples
> 
> # Krige random data for a specified area using a list of polygons
> library(maps)
Error in library(maps) : there is no package called 'maps'
Execution halted
Packages required but not available:
  'DiceKriging', 'randtoolbox', 'rgenoud', 'pbivnorm', 'anMC',
  'mvtnorm'

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: 'pbapply', 'testthat'
Package unavailable to check Rd xrefs: 'pbapply'
Running 'testthat.R'
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: 'rARPACK'

Package suggested but not available for checking: 'testthat'

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

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

Package suggested but not available for checking: 'RUnit'

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'amap', 'FactoClass', 'foreach', 'LICORS', 'testthat'
kselection: no visible global function definition for 'txtProgressBar'
kselection: no visible global function definition for
  'setTxtProgressBar'
plot.Kselection: no visible global function definition for 'lines'
plot.Kselection: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ##
  > ##  Unit testing file
  > ##
  > ##  Created by Daniel Rodriguez Perez on 7/12/2014.
  > ##
  > ##  Copyright (c) 2014 Daniel Rodriguez Perez.
  > ##
  > ##  This program is free software: you can redistribute it and/or modify
  > ##  it under the terms of the GNU General Public License as published by
  > ##  the Free Software Foundation, either version 3 of the License, or
  > ##  (at your option) any later version.
  > ##
  > ##  This program is distributed in the hope that it will be useful,
  > ##  but WITHOUT ANY WARRANTY; without even the implied warranty of
  > ##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > ##  GNU General Public License for more details.
  > ##
  > ##  You should have received a copy of the GNU General Public License
  > ##  along with this program.  If not, see <http://www.gnu.org/licenses/>
  > ## 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'dgof'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'Rcpp'

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

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:
  'FNN', 'kernlab', 'mclust', 'multicool', 'mvtnorm', 'plot3D',
  'pracma'

Packages suggested but not available for checking:
  'geometry', 'misc3d', 'oz', 'rgl'

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

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

Package suggested but not available for checking: 'kst'

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

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

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

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

Package suggested but not available for checking: 'Rgraphviz'

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

Packages suggested but not available for checking:
  'jpeg', 'tclust', 'knitr'

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

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: 'lme4', 'XML'
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'XML' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
auc: no visible global function definition for 'approx'
kulife.colors: no visible global function definition for 'palette'
rootonorm: no visible global function definition for 'sd'
rootonorm: no visible global function definition for 'hist'
rootonorm: no visible global function definition for 'pnorm'
rootonorm: no visible global function definition for 'dnorm'
rootonorm: no visible global function definition for 'rect'
rootonorm: no visible global function definition for 'lines'
rootonorm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approx dnorm hist lines palette pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
Running examples in 'kulife-Ex.R' failed
The error most likely occurred in:

> ### Name: write.xml
> ### Title: Write a data frame in XML format
> ### Aliases: write.xml
> ### Keywords: file
> 
> ### ** Examples
> 
> data(trees)
> write.xml(trees, file="mydata.xml")
Loading required package: XML
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'XML'
Error in write.xml(trees, file = "mydata.xml") : 
  package XML must be installed
Execution halted
Packages required but not available:
  'labstatR', 'matrixcalc', 'polynom', 'expm'

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

Package suggested but not available for checking: 'rockchalk'

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: 'hydroGOF'

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:
  'RUnit', 'R.rsp', 'lme4', 'xtable', 'abind', 'pracma', 'VGAM',
  'copula', 'mvtnorm', 'Hmisc', 'RColorBrewer', 'zoo', 'doParallel',
  'Exact', 'survey'

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

> ### Name: DMHeatMap
> ### Title: Better Heatmap Function
> ### Aliases: DMHeatMap
> 
> ### ** Examples
> 
> 
> cor=matrix(runif(15),5,3)
> breaks=c(-1,-.7,-.5,-.3,-.1,.1,.3,.5,.7,1)
> hU=DMHeatMap(cor, trace="none", symm=FALSE,dendrogram="none", col=RColorBrewer::brewer.pal(
+     length(breaks)-1,"RdYlGn"), distfun = function(c) as.dist(1 - c), cexRow =1.5, cexCol =1.5, 
+     lmat=rbind( c(2, 1), c(4,3) ), lhei=c(4, 1 ), breaks=breaks, margins=c(2,2), key = FALSE, 
+     Rowv=NA, lower.left.only=FALSE)
Error in loadNamespace(x) : there is no package called 'RColorBrewer'
Calls: DMHeatMap ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Warning in par(usr) : argument 1 does not name a graphical parameter
Execution halted
Package suggested but not available for checking: 'polynom'
Packages required but not available: 'digest', 'kzft'

Package suggested but not available for checking: 'polynom'

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

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

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

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

VignetteBuilder 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.
Packages required but not available: 'mixtools', 'ggplot2'

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

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

Package suggested but not available for checking: 'heavy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'igraph', 'aricode', 'caret', 'glmnet', 'ggplot2',
  'cvTools', 'RcppArmadillo'

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

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

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

VignetteBuilder 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', 'ggraph'

Packages suggested but not available for checking:
  'isdals', 'estimability', 'dobson', 'tidyverse'

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

Package suggested but not available for checking: 'optpart'

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

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

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

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

VignetteBuilder 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:
  'testthat', 'roxygen2', 'magrittr', 'rlang', '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: 'pdist'

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: 'combinat', 'lpSolve'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'tests-all.R'
Running the tests in 'tests/tests-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'sp', 'maptools', 'data.table', 'rgdal', 'rgeos', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'cld2', 'magrittr', 'stopwords', '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.
Package required but not available: 'knitr'

Package suggested but not available for checking: 'Rcmdr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'scatterplot3d', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'FrF2'

VignetteBuilder 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', 'statmod'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'httptest', '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:
  'magrittr', 'broom', 'dplyr', 'ggplot2', 'ggtext', 'patchwork',
  'lubridate', 'minpack.lm', 'pracma', 'rlang', 'segmented', 'stringr',
  'tidyr', 'forcats'

Packages suggested but not available for checking:
  'bsplus', 'covr', 'datapasta', 'glue', 'knitr', 'miniUI',
  'rhandsontable', 'rmarkdown', 'shiny', 'shinyjs', 'shinyWidgets',
  'spelling', 'testthat'

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

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

Packages suggested but not available for checking:
  'cubature', 'maptools', 'raster', 'rgdal', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'L1pack'

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', 'yaml'

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', 'rappdirs', 'lazyeval', 'purrr', 'magrittr', 'sf', 'curl',
  'stringr', 'tibble', 'tidyr', 'memoise', 'rlang', 'progress', 'qs'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'devtools', 'R.rsp', 'printr',
  'ggplot2'

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: 'tgp'

Packages suggested but not available for checking:
  'mvtnorm', 'akima', 'lhs', 'crs', 'DiceOptim'

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

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

Packages suggested but not available for checking:
  'ggplot2', 'googleVis', 'data.table', 'vcd', 'reshape2', 'tidyr',
  'knitr', 'rmarkdown', 'car'

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

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

Package suggested but not available for checking: 'R2jags'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'mice', 'GPArotation', 'testthat'
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  'GPArotation' 'mice'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
angoff: no visible global function definition for 'cov2cor'
angoff: no visible global function definition for 'runif'
cov.lambda4: no visible global function definition for 'cov2cor'
cov.lambda4: no visible global function definition for 'median'
guttman: no visible global function definition for 'cov2cor'
impute.cov: no visible global function definition for 'cov'
impute.cov: no visible global function definition for 'complete'
impute.cov: no visible global function definition for 'mice'
kristof: no visible global function definition for 'cov2cor'
kristof: no visible global function definition for 'runif'
lambda1: no visible global function definition for 'cov2cor'
lambda2: no visible global function definition for 'cov2cor'
lambda3: no visible global function definition for 'cov2cor'
lambda3: no visible binding for global variable 'sd'
lambda5: no visible global function definition for 'cov2cor'
lambda6: no visible global function definition for 'cov2cor'
omega.tot: no visible global function definition for 'cov2cor'
omega.tot: no visible global function definition for 'factanal'
quant.lambda4: no visible global function definition for 'cov2cor'
quant.lambda4: no visible global function definition for 'runif'
quant.lambda4: no visible global function definition for 'quantile'
raju: no visible global function definition for 'cov2cor'
raju: no visible global function definition for 'runif'
user.lambda4: no visible global function definition for 'runif'
user.lambda4: no visible binding for global variable 'sd'
Undefined global functions or variables:
  complete cov cov2cor factanal median mice quantile runif sd
Consider adding
  importFrom("stats", "cov", "cov2cor", "factanal", "median", "quantile",
             "runif", "sd")
to your NAMESPACE file.
Running examples in 'Lambda4-Ex.R' failed
The error most likely occurred in:

> ### Name: omega.tot
> ### Title: Compute McDonald's Omega Total
> ### Aliases: omega.tot
> 
> ### ** Examples
> 
> omega.tot(Rosenberg, factors=1)
Loading required package: GPArotation
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'GPArotation'
Error in omega.tot(Rosenberg, factors = 1) : 
  require(GPArotation) is not TRUE
Calls: omega.tot -> stopifnot
Execution halted
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: 'formatR'

Package suggested but not available for checking: 'testit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'purrr', 'abind', 'ggplot2', 'readr', 'stringr', 'lubridate',
  'narray', 'fANCOVA', 'imputeTS', 'modeest', 'scales', 'tictoc',
  'bizdays', 'torch'

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

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

VignetteBuilder 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', 'lamW', 'RColorBrewer', 'reshape2', 'Rcpp'

Packages suggested but not available for checking:
  'Rsolnp', 'nortest', 'numDeriv', 'testthat', 'data.table', 'moments',
  'knitr', 'markdown', 'vars'

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'CDM', 'Rcpp', 'sirt', 'RcppArmadillo'

Packages suggested but not available for checking:
  'coda', 'expm', 'numDeriv', 'STARTS', 'TAM'

Packages which this enhances but not available for checking:
  'lavaan', 'lme4'

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

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:
  'matrixStats', 'mlr', 'parallelMap', 'sp', 'geoR', 'plyr', 'rgdal',
  'gdalUtils', 'raster', 'ranger', 'forestError', 'xgboost', 'kernlab',
  'glmnet', 'ParamHelpers', 'spdep', 'maptools'

Packages suggested but not available for checking:
  'nabor', 'meteo', 'mda', 'psych', 'fossil', 'rjson', 'spatstat',
  'spatstat.core', 'maxlike', 'RCurl', 'deepnet', 'RSAGA', 'plotKML'

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

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

VignetteBuilder 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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgdal', 'sp', 'lmodel2'

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

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

Packages which this enhances but not available for checking: 'stars', '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: 'raster', 'Rcpp'

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

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

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

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:
  'sp', 'Rcpp', 'mvtnorm', 'fields', 'splancs', 'sf', 'DBI', 'RSQLite',
  'foreach', 'doParallel', 'testthat'

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

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

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

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

Packages suggested but not available for checking:
  'shiny', 'GPArotation', 'tourr', 'liminal', 'geozoo',
  'palmerpenguins', 'RANN', 'ggplot2', 'dplyr', 'tibble', 'knitr',
  'rmarkdown', 'airway', 'limma', 'edgeR', 'EnsDb.Hsapiens.v86',
  'AnnotationDbi'

VignetteBuilder 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', 'attempt', 'curl'

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 suggested but not available for checking:
  'e1071', 'rms', 'Hmisc', 'zipfR', 'lme4', 'multcomp', 'lmerTest',
  'optimx'
Packages required but not available:
  'callr', 'collections', 'fs', 'jsonlite', 'lintr', 'R6', 'roxygen2',
  'stringi', 'styler', 'xml2', 'xmlparsedata'

Packages suggested but not available for checking:
  'covr', 'magrittr', 'mockery', 'processx', 'purrr', 'testthat',
  'withr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tinytest'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'tidyr', 'reshape2', 'ggplot2', 'rlang', 'R.matlab'

Packages suggested but not available for checking:
  'covr', '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: 'polynom', 'orthopolynom'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'h2o', 'httr', 'jsonlite', 'lubridate',
  'magrittr', 'openxlsx', 'patchwork', 'pROC', 'rlang', 'rpart.plot',
  'rvest', 'stringr', 'tidyr', 'yaml'

Packages suggested but not available for checking:
  'beepr', 'DALEX', 'DBI', 'forecast', 'googleAuthR', 'googlesheets4',
  'knitr', 'quantmod', 'plotly', 'rdrop2', 'rmarkdown', 'rtweet', 'tm',
  'wordcloud'

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: 'imager', 'dplyr'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'config.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'dplyr'

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: 'data.table', 'treemap', 'xlsx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
betabreaker: no visible global function definition for 'predict'
coef.lars: no visible global function definition for 'predict'
cv.lars: no visible global function definition for 'predict'
cv.lars: no visible binding for global variable 'var'
error.bars: no visible global function definition for 'segments'
plot.lars: no visible global function definition for 'matplot'
plot.lars: no visible global function definition for 'title'
plot.lars: no visible global function definition for 'abline'
plot.lars: no visible global function definition for 'axis'
predict.lars: no visible global function definition for 'approx'
Undefined global functions or variables:
  abline approx axis matplot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
Package required but not available: 'Rcpp'

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

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

Package suggested but not available for checking: 'snowfall'

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

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

Packages suggested but not available for checking: 'covTest', 'lars'

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

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

Package suggested but not available for checking: 'ltm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pcaPP', 'fMultivar', 'mnormt', 'chebpol', 'heatmaply', 'ggplot2',
  'plotly'

Packages suggested but not available for checking:
  'microbenchmark', 'rmarkdown', 'markdown', '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:
  'Rcpp', 'pracma', 'glmnet', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'network', 'ergm', 'sna', 'mvtnorm', 'abind', 'coda',
  'statnet.common'

Packages suggested but not available for checking:
  'snowFT', 'rgl', 'heplots', 'rlecuyer', 'ergm.userterms'

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ggplot2', 'rmarkdown', 'purrr', 'tibble',
  'reactable', 'htmltools', 'RCurl', 'rlang', '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: 'fs', 'rprojroot'

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

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

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'rmarkdown', 'rcmdcheck', 'pkgdown',
  'devtools', 'lme4', 'covr', 'lintr', 'tinytex', 'longitudinalData',
  'kml', 'lcmm', 'longclust', 'mixtools', 'flexmix', 'fda', 'funFEM',
  'gridExtra', 'igraph', 'crimCV', 'akmedoids', 'dtwclust', 'mixAK',
  'clusterCrit', 'mclust', 'mclustcomp', 'psych', 'qqplotr',
  'doParallel', 'simTool', 'dplyr', 'ggplot2', 'caret', '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:
  'magrittr', 'stringr', 'mpoly', 'ggplot2', 'memoise', 'dplyr',
  'usethis', 'glue'

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:
  'spatstat', 'spatstat.geom', 'splancs', 'spdep', 'spam', 'sp',
  'spatialreg', 'sf'

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

Packages suggested but not available for checking:
  'maps', 'mapproj', 'deldir', 'tripack', 'quantreg', 'zoo'

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

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

Package which this enhances but not available for checking: 'chron'
Package unavailable to check Rd xrefs: 'zoo'
Packages required but not available:
  'lavaan', 'DiagrammeR', 'stringr', 'magrittr'

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

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

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

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

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

Packages suggested but not available for checking:
  'testthat', 'mice', 'mitools'

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

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: 'Lavash', 'pracma', 'CVXR'

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

Packages suggested but not available for checking:
  'Rgraphviz', 'data.table', 'ellipse', 'fields', 'geepack', 'gof',
  'graph', 'knitr', 'bookdown', 'rmarkdown', 'igraph', 'lava.tobit',
  'lavaSearch2', 'lme4', 'magrittr', 'mets', 'optimx', 'polycor',
  'quantreg', 'rgl', 'R.rsp', 'testthat', 'visNetwork', '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:
  'ggplot2', 'lava', 'doParallel', 'multcomp', 'mvtnorm', 'Rcpp',
  'reshape2', 'sandwich', 'RcppArmadillo'

Packages suggested but not available for checking:
  'data.table', 'foreach', 'lme4', 'lmerTest', 'numDeriv', 'pbapply',
  'pbkrtest', 'R.rsp', 'riskRegression', 'testthat'

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

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

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

Packages suggested but not available for checking:
  'knitr', '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: 'Kendall', 'mvtnorm', 'Rdpack'

Package suggested but not available for checking: 'fBasics'

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

Packages suggested but not available for checking:
  'distillery', 'eva', 'evd', 'evir', 'extRemes', 'fExtremes', 'ismev',
  'knitr', 'mev', 'POT', 'rmarkdown', 'testthat', 'texmex'

VignetteBuilder 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', 'stars', 'sf', 'dplyr', 'scico', 'ggplot2', 'ggnewscale'

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

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

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

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

Package suggested but not available for checking: 'forecast'

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

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

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

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

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'stringr', 'dplyr', 'tibble', 'lubridate', 'ggplot2', 'h2o',
  'ReinforcementLearning', 'openssl', 'lifecycle'

Packages suggested but not available for checking:
  'testthat', 'covr', 'magrittr', 'data.table', 'bit64'

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

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', 'numDeriv', 'RcppArmadillo'

Packages suggested but not available for checking:
  'optimx', 'microbenchmark', 'testthat', 'knitr', 'pkgbuild',
  'rmarkdown', 'RcppArmadillo'

VignetteBuilder 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: 'actuar'

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

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

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

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

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', 'gridExtra', 'plotrix', 'Rcpp', 'RColorBrewer',
  'shiny', 'tidyr'

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

VignetteBuilder 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', 'rms', 'kinship2'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'png', 'ggrepel',
  'showtext', 'leaflet', 'leaflet.extras'

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

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

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

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

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

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

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: '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.
Packages required but not available: 'Rcpp', 'BH'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'NormPsy', 'ggplot2', 'ggpubr', 'dplyr',
  'gridExtra'

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

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

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

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

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

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

Packages suggested but not available for checking: 'R2WinBUGS', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lavaan', 'dplyr', 'tibble', 'magrittr', 'rlang', 'tidyr', 'ggplot2',
  'broom', 'semPlot', 'stringr', 'purrr', 'data.table', 'utf8'

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

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

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

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: 'quantmod', 'TTR', 'xts', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RUnit', 'data.table', 'entropy', 'foreach', 'iterators', 'iterpc',
  'kSamples', 'car', 'gmp'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'rmarkdown', 'testthat', 'roxygen2',
  '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:
  'batchtools', 'checkmate', 'colorspace', 'data.table', 'dendextend',
  'fs', 'future', 'lda', 'parallelMap', 'progress'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'reshape2', 'ggplot2', 'penalized'
Packages required but not available:
  'beepr', 'broom', 'chinese.misc', 'dplyr', 'DT', 'highcharter',
  'htmlwidgets', 'ldatuning', 'plotly', 'purrr', 'quanteda', 'shiny',
  'shinyalert', 'shinyBS', 'shinycssloaders', 'shinydashboard',
  'shinyjs', 'shinyWidgets', 'SnowballC', 'stringr', 'textmineR',
  'tidyr', 'tidytext', 'tm', 'topicmodels'

Packages suggested but not available for checking:
  'knitr', 'RColorBrewer', 'rmarkdown', 'Rmpfr', 'scales', '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: 'lvec', 'Rcpp', 'BH'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'digest', 'extraDistr', 'lubridate', 'magrittr', 'memoise',
  'mvtnorm', 'progress', 'topicmodels', 'viridis'

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

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

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

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: 'proxy', 'RJSONIO'

Packages suggested but not available for checking:
  'mallet', 'lda', 'topicmodels', 'gistr', 'servr', 'shiny', 'knitr',
  'rmarkdown', 'digest', 'htmltools'

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

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

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

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

VignetteBuilder package required for checking but not installed: 'R.rsp'
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'RcppProgress', 'rgen', 'gtools', 'LaplacesDemon', 'dplyr',
  'plyr', 'tidyr', 'ggplot2', 'latex2exp', 'reshape2', 'RColorBrewer',
  'RcppArmadillo'

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

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

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

Packages suggested but not available for checking:
  'rtracklayer', 'GenomicRanges', 'GenomeInfoDb', 'IRanges', 'ggplot2',
  'vcfR'

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

Packages suggested but not available for checking:
  'knitr', 'testthat', 'depmixS4', 'roxygen2', 'R.rsp', 'shape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'caret', 'caretEnsemble', 'lares', 'corrplot',
  'RColorBrewer', 'resample', 'glmnet', 'earth', 'kernlab', 'gbm',
  'Cubist', 'randomForest'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  '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:
  'keras', 'devtools', 'reticulate', 'tensorflow'

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: 'nleqslv'

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

> ### Name: AOP
> ### Title: Function to Average Orthogonal Projection Matrices
> ### Aliases: AOP
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> ## Ex.1
> ##
> library(dr)
Error in library(dr) : there is no package called 'dr'
Execution halted
Packages required but not available:
  'Rcpp', 'foreach', 'doParallel', 'ashr', 'corrplot', 'lpSolve',
  'abind', 'modeest', 'matrixStats', 'RcppArmadillo'

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

VignetteBuilder 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', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'GA', 'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'patchwork',
  'doFuture', 'future'

VignetteBuilder 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', 'R6'

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

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

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

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown', 'shinytest', 'dplyr',
  '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:
  'base64enc', 'geojsonsf', 'htmltools', 'htmlwidgets', 'leaflet',
  'raster', 'sf', 'png'

Packages suggested but not available for checking:
  'clipr', 'gdalUtils', 'leafgl', 'mapdeck', 'plainview', 'stars'

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

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

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

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

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

Package suggested but not available for checking: 'htmlwidgets'

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

Packages suggested but not available for checking:
  'jsonlite', 'shiny', 'sf', 'geojsonsf', 'sp', 'testthat', 'covr'

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

Packages suggested but not available for checking: 'jsonlite', 'readr'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'shiny', 'manipulateWidget',
  '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: 'htmlwidgets', 'htmltools'

Packages suggested but not available for checking:
  'leaflet', 'testthat', 'magrittr', 'raster', 'rgdal', '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: 'htmltools', 'htmlwidgets'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'V8', 'jsonlite', '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:
  'base64enc', 'crosstalk', 'htmlwidgets', 'htmltools', 'magrittr',
  'markdown', 'png', 'RColorBrewer', 'raster', 'scales', 'sp',
  'viridis', 'leaflet.providers'

Packages suggested but not available for checking:
  'knitr', 'maps', 'sf', 'shiny', 'rgdal', 'rgeos', 'R6', 'RJSONIO',
  'purrr', 'testthat', 's2'

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

Packages suggested but not available for checking: 'httr', 'rgdal', 'sp'

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

Package suggested but not available for checking: 'testthat'

Packages which this enhances but not available for checking:
  'geojsonio', 'mapedit', 'mapview', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'brew', 'htmltools', 'htmlwidgets', 'sf', 'svglite',
  'uuid'

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

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

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

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

Package suggested but not available for checking: 'geojsonio'

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

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.
Packages required but not available: 'igraph', 'foreach'

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

Package suggested but not available for checking: 'rjags'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'LEAP_Vignette.Rnw' using Sweave

Error: processing vignette 'LEAP_Vignette.Rnw' failed with diagnostics:
 chunk 10 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'LEAP_Vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'biglm'
Packages required but not available:
  'conicfit', 'doParallel', 'foreach', 'jpeg', 'opencpu'

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

Packages suggested but not available for 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:
  'knitr', 'rmarkdown', 'testthat'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'magick', 'crayon'

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Packages suggested but not available for checking:
  'ChemoSpec', 'chemometrics', 'kableExtra', 'knitr', 'tinytest',
  'roxut', 'bookdown', 'rmarkdown', 'plot3D', 'ade4', 'plotrix',
  'latex2exp', 'plotly', 'xtable', 'htmlwidgets'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'gtools', 'phytools'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'withr', 'rappdirs', 'rprojroot', 'jsonlite', 'htmltools',
  'htmlwidgets', 'evaluate', 'knitr', 'markdown', 'shiny', 'rmarkdown',
  'ellipsis', 'checkmate', 'renv'

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

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'glmmTMB', 'lme4', 'MuMIn', 'pscl', 'SparseM', 'VGAM',
  'RcppArmadillo', 'BH'

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

VignetteBuilder 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'

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

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

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

Packages suggested but not available for checking:
  'numDeriv', 'testthat', 'knitr', 'rmarkdown', 'doMC', 'doParallel',
  '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: 'curl', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr', 'magrittr', 'purrr', 'stringr',
  '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:
  'formula.tools', 'pROC', 'foreach', 'snow', 'doSNOW', 'iterators',
  'Hmisc', 'RColorBrewer', 'glmnet', 'lme4'

Packages suggested but not available for 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: '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:
  'readr', 'rlang', 'stringr', 'glue', 'httr', 'dplyr', 'rappdirs'

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

VignetteBuilder 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', 'Matrix.utils', 'Rcpp', 'sccore', 'RcppArmadillo',
  'RcppEigen'

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

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

Packages suggested but not available for checking:
  '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: 'reticulate', 'igraph'

Packages suggested but not available for checking:
  'bipartite', 'covr', 'data.table', 'devtools', 'graphsim', 'knitr',
  'multiplex', 'multinet', 'markdown', 'network', 'RColorBrewer',
  'rmarkdown', 'spelling', '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: 'Rcpp', 'abind', '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: 'deSolve', 'ggplot2', 'gridExtra'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'dplyr', 'tidyr', 'future',
  'furrr', 'RColorBrewer', 'microbenchmark'

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'stringr', '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: 'magrittr', 'tidyselect', '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: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', '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:
  'fs', 'cli', 'usethis', 'jsonlite', 'roxygen2'

Packages suggested but not available for checking:
  'bslib', 'yaml', 'covr', 'sass', 'htmltools', 'packer', 'shiny',
  'testthat', 'pkgload'

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

Packages suggested but not available for checking:
  'covr', 'knitr', 'maptools', 'rmarkdown', 'sf', 'sp', 'testthat',
  'viridis'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'latticeExtra', 'robustbase', 'ellipse', 'leaps', 'openxlsx',
  'colorspace', 'shiny', 'knitr', 'viridisLite'

Packages suggested but not available for checking:
  'rmarkdown', 'wesanderson', 'haven', 'readODS', 'triangle'

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 unavailable to check Rd xrefs: 'MESS'
'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:
  'raster', 'maps', 'XML', 'geosphere', 'fields', 'maptools', 'sp',
  'rgdal', 'rgeos'

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

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

Packages suggested but not available for checking:
  'knitr', 'pkgdown', '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:
  'tidyverse', 'knitr', 'rmarkdown', 'testthat', 'future.apply',
  'tictoc'

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
Note: found 3 marked UTF-8 strings
Packages required but not available: 'data.table', 'syuzhet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'pbapply', 'quanteda', 'quanteda.textstats',
  'stringdist', 'stringi', 'tibble'

Packages suggested but not available for checking:
  'corpustools', 'covr', 'diffobj', 'dplyr', 'RSQLite', 'testthat',
  'tidytext', 'tm', 'kableExtra', 'knitr', 'pdftools', 'rmarkdown',
  'spelling', 'striprtf', '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: 'ggplot2', 'dplyr', 'tidyr'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'shiny', 'shinyjs', 'shinythemes', 'shinyFiles', 'shinyMobile',
  'EBImage', 'DT', 'ggplot2', 'fs'

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

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

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

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

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

Packages suggested but not available for checking: 'LFDR.MLE', 'testthat'

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

Packages suggested but not available for checking:
  'knitr', 'digest', 'igraph', 'plm', 'cubature', 'numDeriv',
  'data.table', 'alpaca', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'foreach', 'forecast', 'plyr', 'tseries', 'e1071', 'zoo'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'rmarkdown', 'knitr', 'RSpectra', 'ggplot2', 'readr',
  'purrr', 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xts', 'lmom', 'lmomRFA', 'dygraphs', 'zoo', 'latticeExtra', 'plyr'

Package suggested but not available for checking: 'testthat'

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:
  'spatstat.geom', 'spatstat.core', 'spatstat', 'spatstat.utils', 'sp',
  'raster', 'RandomFields', 'iterators', 'ncdf4', 'rpanel', 'fields',
  'maptools', 'rgeos'

Packages suggested but not available for checking:
  'sparr', 'rgdal', 'gpclib'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'RCurl', 'rstan', 'rstantools', 'bayesplot',
  'ggplot2', 'gridExtra', 'BH', 'RcppEigen', 'StanHeaders'

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:
  'mvtnorm', 'localgauss', 'logspline', 'ggplot2', 'ks', 'np',
  'tseries'

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: 'ggplot2'
Packages required but not available: 'data.table', 'lgr'

Packages suggested but not available for checking:
  'covr', 'DBI', 'gmailr', 'jsonlite', 'RMariaDB', 'RPostgres',
  'RPushbullet', 'RSQLite', 'rsyslog', 'sendmailR', 'testthat',
  'knitr', 'rmarkdown'

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

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

Packages suggested but not available for checking:
  'cli', 'covr', 'crayon', 'data.table', 'desc', 'future',
  'future.apply', 'glue', 'jsonlite', 'knitr', 'rmarkdown', 'rotor',
  'rprojroot', 'testthat', 'tibble', 'whoami', 'yaml'

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

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

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: 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'assertthat', 'DoE.base', 'knitr', 'rmarkdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'phangorn', 'RColorBrewer', 'ape', 'plyr', 'matlab', 'biomaRt',
  'distances', 'arules', 'e1071', 'proxy', 'gplots'

Packages suggested but not available for checking:
  'mclust', 'fpc', 'NbClust', 'modeest', 'pastecs', 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'curl', 'pbapply', 'stringr', 'xml2'

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

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

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

Package suggested but not available for checking: 'coin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'SparseM', 'testthat'
Package unavailable to check Rd xrefs: 'LiblineaR'
Running 'testthat.R'
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: 'SparseM'
Packages required but not available: 'BiocManager', 'remotes'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'readr', 'readxl', 'haven', 'openxlsx', 'crayon', 'dplyr', 'tibble',
  'Rcpp', 'data.table'

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

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'
Running 'testthat.R'
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', 'RcppGSL'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RColorBrewer', 'mvtnorm', 'zoo', 'FNN', 'fields', 'locfit'

Packages suggested but not available for checking:
  'huge', 'RANN', 'yaImpute', 'itertools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'sp', 'raster', 'imager', 'leaps', 'gvlma', 'car', 'reldist', 'lidR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'classInt', 'data.table', 'glue', 'lazyeval', 'raster', 'Rcpp',
  'rgl', 'rlas', 'sf', 'sp', 'stars', 'terra', 'BH', 'RcppArmadillo'

Packages suggested but not available for checking:
  'EBImage', 'future', 'geometry', 'gstat', 'RCSF', 'RMCC', 'rgdal',
  'mapview', 'mapedit', 'progress', '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: 'markovchain', 'Rcpp'

Packages suggested but not available for checking:
  'demography', 'forecast', 'testthat', 'knitr', 'formatR', 'StMoMo',
  '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: 'TraMineR'

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

Packages suggested but not available for checking:
  'covr', 'crayon', 'lintr', 'tidyverse', 'knitr', 'rmarkdown',
  'testthat', 'tibble', '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: 'Hmisc', 'optimx', 'BB'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'MortalityTables', 'objectProperties', 'lubridate', 'openxlsx',
  'dplyr', 'scales', 'abind', 'stringr', 'rlang', 'kableExtra',
  'pander', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'magrittr', '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:
  'ggplot2', 'shiny', 'dplyr', 'lubridate', 'modelr', 'stringr',
  'tidyr', 'lazyeval', 'R6', 'fitbitScraper', 'tibble', 'plyr'

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

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

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

Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'

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

Package suggested but not available for checking: 'fracdiff'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'yaml', 'knitr', 'rmarkdown', 'stringr', '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:
  'curl', 'httr', 'assertthat', 'jsonlite', 'crayon'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'matrixStats', '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: 'R6', 'data.table', '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: 'RJSONIO', 'RCurl', 'R6', 'httr'

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

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

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:
  'hetGP', 'laGP', 'doParallel', 'foreach'

Package suggested but not available for checking: 'lhs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'purrr', 'tibble', 'dplyr', 'RSelenium', 'raster', 'magrittr',
  'rvest', 'xml2'

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

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

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

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

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

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'xtable', 'psych', 'reshape2', 'gridExtra', 'plyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'caret', 'dplyr', 'gbm', 'ggplot2', 'glmnet', 'h2o', 'impute',
  'infotheo', 'limma', 'M3C', 'Metrics', 'MLmetrics', 'princurve',
  'pathview', 'plyr', 'preprocessCore', 'pROC', 'RCy3', 'reticulate',
  'reshape', 'RWeka', 'scales', 'stringr', 'survminer'

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

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

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

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FNN', 'stringi', 'beepr', 'ggplot2', 'keras', 'dplyr', 'readr',
  'textclean', 'tm', 'e1071', 'SnowballC', 'data.table', 'fastmatch',
  'neuralnet'

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

Packages suggested but not available for checking:
  'xgboost', 'testthat', 'mlr', 'h2o', 'text2vec', 'covr', 'knitr',
  'rmarkdown', 'sessioninfo', 'magick', 'keras', 'htmlwidgets',
  'shiny', 'shinythemes', '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:
  'tourr', 'shiny', 'vegawidget', 'miniUI', 'jsonlite', 'rlang',
  'dplyr', 'matrixStats'

Packages suggested but not available for checking:
  'Rtsne', 'knitr', 'rmarkdown', 'covr', 'ggplot2', '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: 'httr', 'jsonlite', 'R6'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'ashr', 'checkmate', 'data.table', 'DESeq2', 'foreach',
  'HDInterval', 'iterators', 'limma', 'mashr', 'pbs', 'zeallot'

Packages suggested but not available for checking:
  'cowplot', 'knitr', 'doParallel', 'ggplot2', 'glue', 'qs',
  '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: 'pbs'

Packages suggested but not available for checking:
  'annotate', 'data.table', 'foreach', 'ggplot2', 'knitr', 'limma',
  'matrixStats', 'org.Mm.eg.db', 'qs', 'rmarkdown', 'testthat'

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

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

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

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'
class.calib: no visible global function definition for 'lm'
class.calib: no visible global function definition for 'coef'
class.calib: no visible global function definition for 'qt'
hoad.calib: no visible global function definition for 'lm'
hoad.calib: no visible global function definition for 'anova'
hoad.calib: no visible global function definition for 'qt'
hoad.calib: no visible global function definition for 'rnorm'
huntlam.calib: no visible global function definition for 'lm'
huntlam.calib: no visible global function definition for 'anova'
huntlam.calib: no visible global function definition for 'rnorm'
huntlam.calib: no visible global function definition for 'qnorm'
inver.calib: no visible global function definition for 'lm'
inver.calib: no visible global function definition for 'coef'
inver.calib: no visible global function definition for 'anova'
inver.calib: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  anova coef lm qnorm qt rnorm
Consider adding
  importFrom("stats", "anova", "coef", "lm", "qnorm", "qt", "rnorm")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

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

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

Package suggested but not available for checking: 'fitdistrplus'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'sandwich', 'dplyr', 'ggplot2', 'viridis', 'tidyr', 'readr',
  'forecast'

Package suggested but not available for checking: 'testthat'

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

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

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

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

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

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

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

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

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

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

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: 'kableExtra', 'knitr', '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', 'RcppParallel'

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'sp', 'rgeos', 'rgdal',
  'ggplot2', 'ape'

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

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

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rgdal', 'sp', 'RSAGA', 'rgrass7', 'curl',
  'listviewer', '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: 'qtl', 'plotrix', 'RColorBrewer'

Packages suggested but not available for checking:
  'rmarkdown', '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:
  'igraph', 'RColorBrewer', 'dynamicTreeCut'

Packages suggested but not available for checking: 'fastcluster', '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: 'nloptr', 'spBayes'

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

Packages suggested but not available for checking:
  'BGData', 'ff', 'bigmemory', 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
gcomb: no visible global function definition for 'complete.cases'
linkim: no visible global function definition for 'runif'
missing.dist: no visible global function definition for
  'complete.cases'
pgdata1: no visible global function definition for 'barplot'
pgdata1: no visible global function definition for 'layout'
pgdata1: no visible global function definition for 'par'
pgdata1: no visible global function definition for 'rainbow'
singim: no visible global function definition for 'complete.cases'
singim: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot complete.cases layout par rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "barplot", "layout", "par")
  importFrom("stats", "complete.cases", "runif")
to your NAMESPACE file.
Packages required but not available: 'igraph', 'intergraph'

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:
  'shiny', 'visNetwork', 'infotheo', 'minerva', 'energy', 'mclust',
  'rAmCharts', 'pbapply', 'ggplot2', 'dplyr', 'tidyr', 'shinybusy'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
gen.lms: no visible global function definition for 'na.omit'
plot.idf: no visible global function definition for 'mtext'
plot.idf: no visible global function definition for 'points'
plot.idf: no visible global function definition for 'segments'
plot.idf: no visible global function definition for 'ftable'
plot.idf: no visible global function definition for 'image'
plot.idf: no visible global function definition for 'gray'
plot.idf: no visible global function definition for 'abline'
plot.s.linlir: no visible global function definition for 'mtext'
plot.s.linlir: no visible global function definition for 'polygon'
plot.s.linlir: no visible global function definition for 'points'
plot.s.linlir: no visible global function definition for 'curve'
s.linlir: no visible global function definition for 'na.omit'
s.linlir: no visible global function definition for 'dbinom'
s.linlir: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq points
  polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "points",
             "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
Packages required but not available: 'rmarkdown', 'knitr'

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

VignetteBuilder 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', 'purrr', 'cli', 'shiny', 'magrittr'

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

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

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

Packages suggested but not available for checking:
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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: 'lpSolve'

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

Packages suggested but not available for checking: 'AER', 'gam'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'scales', 'shinythemes', 'iterators'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'shadowtext', 'stringr', 'tableone', 'tidyr'

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

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

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

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.
getMatrix : <anonymous>: 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.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'magrittr', 'zeallot', 'rlang', 'tibble', 'purrr'
Found a .Internal call in the following function:
  'eval'
with calls to .Internal functions
  'eval'

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
Packages unavailable to check Rd xrefs: 'purrr', 'keras'
'LazyData' is specified without a 'data' directory
Running examples in 'listarrays-Ex.R' failed
The error most likely occurred in:

> ### Name: extract_dim
> ### Title: Extract with '[' on a specified dimension
> ### Aliases: extract_dim extract_rows extract_cols
> 
> ### ** Examples
> 
> # extract_rows is useful to keep the same code path for arrays of various sizes
> X <- array(1:8, c(4, 3, 2))
> y <- c("a", "b", "c", "d")
> (Y <- onehot(y))
     a b c d
[1,] 1 0 0 0
[2,] 0 1 0 0
[3,] 0 0 1 0
[4,] 0 0 0 1
> 
> extract_rows(X, 2)
     [,1] [,2]
[1,]    2    6
[2,]    6    2
[3,]    2    6
> extract_rows(Y, 2)
a b c d 
0 1 0 0 
> extract_rows(y, 2)
[1] "b"
> 
> library(zeallot)
Error in library(zeallot) : there is no package called 'zeallot'
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: 'rlang'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'listcompr-Ex.R' failed
The error most likely occurred in:

> ### Name: gen.logical.and
> ### Title: Generate Logical Conditions with List Comprehension
> ### Aliases: gen.logical.and gen.logical.or
> 
> ### ** Examples
> 
> # Returns a_1 == 1 & a_2 == 2 & a_3 == 3
> gen.logical.and(a_i == i, i = 1:3)
a_1 == 1L & (a_2 == 2L & a_3 == 3L)
> 
> # A data frame of tuples (x_1, x_2, x_3, x_4) summing up to 10 with x_i <= x_(i+1)
> gen.data.frame(c(x_1, ..., x_4), x_ = 1:10, x_1 + ... + x_4 == 10, 
+                gen.logical.and(x_i <= x_(i+1), i = 1:3))
  x_1 x_2 x_3 x_4
1   2   2   3   3
2   1   3   3   3
3   2   2   2   4
4   1   2   3   4
5   1   1   4   4
6   1   2   2   5
7   1   1   3   5
8   1   1   2   6
9   1   1   1   7
> 
> # Get all permutations of 1:4
> gen.data.frame(c(a_1, ..., a_4), a_ = 1:4, 
+                gen.logical.and(a_i != a_j, i = 1:4, j = (i+1):4))
   a_1 a_2 a_3 a_4
1    4   3   2   1
2    3   4   2   1
3    4   2   3   1
4    2   4   3   1
5    3   2   4   1
6    2   3   4   1
7    4   3   1   2
8    3   4   1   2
9    4   1   3   2
10   1   4   3   2
11   3   1   4   2
12   1   3   4   2
13   4   2   1   3
14   2   4   1   3
15   4   1   2   3
16   1   4   2   3
17   2   1   4   3
18   1   2   4   3
19   3   2   1   4
20   2   3   1   4
21   3   1   2   4
22   1   3   2   4
23   2   1   3   4
24   1   2   3   4
>                
> # Get again the permutations of 1:4, using filter from dplyr 
> df <- gen.data.frame(c(a_1, ..., a_4), a_ = 1:4)
> dplyr::filter(df, !!gen.logical.and(a_i != a_j, i = 1:3, j = (i+1):4))
Error in loadNamespace(x) : there is no package called 'dplyr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.r'
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', 'yaml'

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

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

VignetteBuilder 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.
Skipping vignette re-building
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'LazyData' is specified without a 'data' directory
Packages required but not available:
  'sandwich', 'VGAM', 'magic', 'gamlss.dist', 'quadprog', 'corpcor',
  'mvtnorm', 'coda', 'arm'

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: 'htmltools', 'htmlwidgets', 'shiny'

Packages suggested but not available for checking:
  'jsonlite', 'miniUI', 'rstudioapi'

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

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

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

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

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

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

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

VignetteBuilder 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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  'purrr', 'rlang', 'yaml', 'rmarkdown'

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', 'purrr', 'jsonlite', 'data.table', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr', 'dplyr', 'breakDown', 'data.table', 'forestmodel', 'shiny',
  'ggplot2', 'gower', 'e1071'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'glmnet', 'covr', 'DALEX', 'RWeka',
  'mda', 'modeltools'

VignetteBuilder 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'

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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:
  'SparseM', 'data.table', 'LiblineaR', 'glmnet', 'glmnetUtils', 'lme4'

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:
  'mlr', 'rJava', 'parallelMap', 'ggplot2', 'checkmate', 'BBmisc',
  'plyr', 'data.table'

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

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

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

Package suggested but not available for checking: 'rgl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'partykit', 'stringr', 'RWeka', 'survey', 'reghelper', 'scales'

Package suggested but not available for checking: 'mlbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rootSolve', 'openxlsx', 'digest', 'svDialogs', 'minpack.lm',
  'ggplot2', 'svglite', 'dplyr', 'nleqslv', 'crayon'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
lm.beta: no visible global function definition for 'coef'
lm.beta: no visible global function definition for 'model.matrix'
lm.beta: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  coef model.frame model.matrix
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix")
to your NAMESPACE file.
Package required but not available: 'evd'

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', 'plyr', 'sommer'

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'PKPDmodels', 'MEMSS', 'testthat', 'ggplot2',
  'mlmRev', 'optimx', 'gamm4', 'pbkrtest', 'HSAUR3', 'numDeriv', 'car',
  'dfoptim', 'statmod', 'rr2', 'semEff', 'tibble'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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  'mlmRev', 'carData', 'lme4', 'merDeriv'

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

> ### Name: g_mlm
> ### Title: Calculates adjusted mlm effect size
> ### Aliases: g_mlm
> 
> ### ** Examples
> 
> 
> library(nlme)
> data(Bryant2016, package = "lmeInfo")
> Bryant2016_RML1 <- lme(fixed = outcome ~ treatment,
+                        random = ~ 1 | school/case,
+                        correlation = corAR1(0, ~ session | school/case),
+                        data = Bryant2016)
> Bryant2016_g1 <- g_mlm(Bryant2016_RML1, p_const = c(0,1), r_const = c(1,1,0,1),
+                        infotype = "expected", returnModel = TRUE)
> summary(Bryant2016_g1)
                                           est      se
Tau.school.school.var((Intercept))     105.619 285.200
Tau.case.case.var((Intercept))           0.000 632.159
cor_params                               0.978   0.015
sigma_sq                              1058.303 678.388
total variance                        1163.922 366.515
(Intercept)                             84.571   9.684
treatmenttreatment                      16.425   2.975
treatment effect at a specified time    16.425   2.975
unadjusted effect size                   0.481   0.122
adjusted effect size                     0.463   0.118
degree of freedom                       20.169        
constant kappa                           0.087        
logLik                               -1133.122        
> print(Bryant2016_g1)
                          est    se
unadjusted effect size  0.481 0.122
adjusted effect size    0.463 0.118
degree of freedom      20.169      
> 
> data(Laski, package = "scdhlm")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'scdhlm'
Calls: data -> find.package
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'numDeriv', 'statmod', 'lmeNBBayes'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'nlmeU', 'ggplot2', 'ggdist', 'HLMdiag', 'purrr', 'forcats',
  'statmod', 'tidyr', 'magrittr'

Packages suggested but not available for checking:
  'lme4', 'testthat', 'mlmRev', 'knitr', 'rmarkdown', 'doParallel',
  '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: 'lme4', 'numDeriv', 'ggplot2'

Package suggested but not available for checking: 'pbkrtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
approx.Z : <anonymous>: no visible global function definition for
  'approx'
smspline: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  approx model.frame
Consider adding
  importFrom("stats", "approx", "model.frame")
to your NAMESPACE file.
Packages required but not available:
  'MultiLCIRT', 'mvtnorm', 'Formula', 'mix', 'diagram', 'mclust',
  'scatterplot3d'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'rmarkdown', '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 unavailable to check Rd xrefs: 'sfsmisc', 'mnormt'
Package required but not available: 'generics'

Packages suggested but not available for checking:
  'bookdown', 'coda', 'covr', 'ggplot2', 'knitr', 'mvtnorm',
  'numDeriv', 'patchwork', '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', 'rstan', 'rstantools', 'Formula', 'loo', 'BH', 'RcppEigen',
  'StanHeaders'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'matrixcalc', 'mnormt', 'plyr', 'doParallel', '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:
  'agridat', 'ggplot2', 'maps', 'Rcpp', 'sp', 'spam'

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', 'lava', 'multcomp', 'numDeriv', 'reshape2',
  'sandwich'

Packages suggested but not available for checking:
  'AICcmodavg', 'copula', 'data.table', 'ggpubr', 'mvtnorm', 'nlmeU',
  'optimx', 'psych', 'Publish', 'qqtest', 'R.rsp', 'testthat'

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

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

Packages suggested but not available for checking:
  'testthat', 'numDeriv', 'mniw', 'knitr', 'rmarkdown', 'bookdown',
  '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: 'lmom', 'pracma', 'ggplot2', 'sf'

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

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

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

Package suggested but not available for checking: 'copBasic'

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: 'lmom', 'stringr'

Packages suggested but not available for checking:
  'rasterList', 'lmomRFA', 'SPEI'

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

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: 'genefilter', 'Biobase', 'progress'

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

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

Packages suggested but not available for checking:
  'car', 'strucchange', 'sandwich', 'dynlm', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nnls', 'cli', 'R6', 'generics', 'origami', 'future', 'progressr',
  'data.table', 'SuperLearner'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown', 'knitr', 'ranger', 'twang',
  '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: 'matrixcalc', 'maxLik'

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

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:
  'shiny', 'shinyjs', 'lmtest', 'scatterplot3d', 'rgl', 'car'

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

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

Package suggested but not available for checking: 'graph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'coda', 'mcmcse'
Packages required but not available:
  'dplyr', 'dygraphs', 'ggplot2', 'lubridate', 'rlang', 'tidyr',
  'tsibble', 'xts', 'zoo'

Packages suggested but not available for checking:
  'brolgar', 'covr', 'fabletools', 'feasts', 'knitr', 'lifecycle',
  'purrr', 'rmarkdown', 'testthat'

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

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

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:
  'png', 'RgoogleMaps', 'OpenStreetMap', 'sp', 'rgdal', 'RColorBrewer',
  'plyr'

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

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

VignetteBuilder 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', 'Rcpp', 'rlang'

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

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

Packages suggested but not available for checking:
  'colorspace', 'RColorBrewer', 'TeachingDemos', 'data.table',
  'ggplot2', 'gridExtra', 'rpart.plot', 'xtable'

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

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

Packages suggested but not available for checking:
  'covr', 'h2o', 'mlbench', 'randomForest', 'testthat'

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

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

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

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

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

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

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'ggplot2'

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: 'interp', 'gam'
Packages required but not available: 'wavethresh', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'lubridate', 'mosaic'
Packages required but not available: 'fda', 'psych'

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

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', 'Rdpack', 'RSpectra', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'rms'

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

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

VignetteBuilder 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'

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

> ### Name: GARI
> ### Title: Graph Adjusted Rand Index
> ### Aliases: GARI
> 
> ### ** Examples
> 
> library(igraph)
Error in library(igraph) : there is no package called 'igraph'
Execution halted
Packages required but not available:
  'dplyr', 'tidyr', 'magrittr', 'rlang', 'ggplot2', 'metR',
  'gridExtra', 'rootSolve', 'viridis'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'futile.logger', 'httr', 'jsonlite', 'knitr', 'lgr', 'logger',
  'logging', 'loggit', 'microbenchmark', 'rlog', 'rmarkdown',
  'rsyslog', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages unavailable to check Rd xrefs: 'httr', 'rsyslog'
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'pander', 'psych', 'dplyr', 'ggplot2', 'rlang', 'stringr',
  'magrittr', 'modules'

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:
  'glm2', 'turboEM', 'itertools2', 'iterators'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'glue', 'pander', 'jsonlite', 'crayon', 'slackr', 'RPushbullet',
  'telegram', 'testthat', 'covr', 'knitr', 'rmarkdown', 'devtools',
  'roxygen2', 'rsyslog', 'shiny', 'callr', 'txtq', 'botor', 'R.utils',
  'syslognet'

Packages which this enhances but not available for checking:
  'logging', 'futile.logger', 'log4r'

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

> ### Name: %except%
> ### Title: Try to evaluate an expressions and evaluate another expression
> ###   on exception
> ### Aliases: %except%
> 
> ### ** Examples
> 
> everything %except% 42
WARN [2022-03-27 05:53:20] Running "42" as "everything" failed: "object 'everything' not found"
[1] 42
> everything <- '640kb'
> everything %except% 42
[1] "640kb"
> 
> Mean(1:10) %except% sum(1:10) / length(1:10)
WARN [2022-03-27 05:53:20] Running "sum(1:10)" as "Mean(1:10)" failed: "could not find function \"Mean\""
[1] 5.5
> Mean(1:10) %except% (sum(1:10) / length(1:10))
WARN [2022-03-27 05:53:20] Running "(sum(1:10)/length(1:10))" as "Mean(1:10)" failed: "could not find function \"Mean\""
[1] 5.5
> Mean(1:10) %except% MEAN(1:10) %except% mean(1:10)
WARN [2022-03-27 05:53:20] Running "MEAN(1:10)" as "Mean(1:10)" failed: "could not find function \"Mean\""
Error in sprintf(fmt, ...) : too few arguments
Calls: %except% ... <Anonymous> -> do.call -> <Anonymous> -> eval -> sprintf
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'crayon'
Running 'run_tests.R'
Running the tests in 'tests/run_tests.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'partykit', 'doParallel', 'data.table', 'foreach', 'iterators'

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

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
EstimateProbability: no visible global function definition for
  'predict'
LOGICOIL: no visible binding for global variable 'pssm'
LOGICOIL: no visible binding for global variable 'LOGICOILfit'
LOGICOIL: no visible binding for global variable 'Model_Parameters'
plot_LOGICOIL: no visible global function definition for 'png'
plot_LOGICOIL: no visible global function definition for 'par'
plot_LOGICOIL: no visible global function definition for 'lines'
plot_LOGICOIL: no visible global function definition for 'axis'
plot_LOGICOIL: no visible global function definition for 'mtext'
plot_LOGICOIL: no visible global function definition for 'legend'
plot_LOGICOIL: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par png
  predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par")
  importFrom("stats", "predict")
to your NAMESPACE file.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'popbio'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rms', 'statmod', 'speedglm', 'RColorBrewer', 'data.table', 'pROC',
  'aod'

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/plotGlm.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:
  'rARPACK', '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:
  'ggplot2', 'knitr', 'rmarkdown', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'fda', 'expm', 'pROC', 'fda.usc'

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

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

Packages suggested but not available for checking:
  'dplyr', 'fastDummies', 'knitr', 'rmarkdown', 'here', '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: 'Rcpp', 'pracma'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
rloglognorm: 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: 'gnm', 'qvcalc'

Packages suggested but not available for checking:
  'survey', 'ellipse', '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:
  'markdown', 'rmarkdown', 'testthat', 'knitr', 'dplyr', 'ggplot2',
  'mvtnorm', 'purrr', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # workaround for error LC_CTYPE failed, using "C" but does not work
  > #https://github.com/r-lib/testthat/issues/86
  > #Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
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
LogrankA: no visible global function definition for 'is.Surv'
LogrankA: no visible global function definition for 'na.omit'
LogrankA: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  is.Surv na.omit pchisq
Consider adding
  importFrom("stats", "na.omit", "pchisq")
to your NAMESPACE file.
Packages required but not available: 'R6', 'cli', 'crayon'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'network', 'ggplot2', 'reshape2', 'intergraph', 'BH'

Packages suggested but not available for checking:
  'testthat', 'inline', 'knitr', 'rmarkdown', 'ergm', 'BH', '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:
  'ggplot2', 'abind', 'irlba', 'pls', 'robust', 'robustbase'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'randomForest', 'latex2exp', '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', 'FNN', 'data.table', 'doParallel', 'foreach', 'proxy',
  'reshape2', 'pracma', 'transport', 'RANN', 'ff', 'aws', 'dbscan',
  'EBImage', 'BH'

Package suggested but not available for checking: 'testthat'

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

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

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

> ### Name: longclustEM
> ### Title: Model-Based Clustering and Classification for Longitudinal Data
> ### Aliases: longclustEM
> ### Keywords: "multivariate" "cluster" "classif"
> 
> ### ** Examples
> 
> library(mvtnorm)
Error in library(mvtnorm) : there is no package called 'mvtnorm'
Execution halted
Packages required but not available:
  'lme4', 'reshape2', 'glmmTMB', 'emmeans', 'bestNormalize', 'ggplot2',
  'stringr', 'magrittr', 'tibble', 'dplyr', 'rlang', 'car', 'rstatix',
  'effsize', 'tidyr', 'patchwork'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'tidyverse', '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:
  'AICcmodavg', 'missForest', 'R2jags', 'rjags'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'clv', 'rgl', 'misc3d'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randomForest', 'mvtnorm', 'latex2exp'

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: 'sfsmisc'

Package which this enhances but not available for checking: 'fracdiff'
Errors in running code in vignettes:
when running code in 'BspecFGN.Rnw'

> op.orig <- options(width = 75, SweaveHooks = list(fig = function() par(mar = c(5.1, 
+     4.1, 1.1, 2.1))), useFancyQuotes = FALSE, continue = "  " .... [TRUNCATED] 

> Sys.setenv(LANGUAGE = "en")

> if (.Platform$OS.type != "windows") Sys.setlocale("LC_MESSAGES", 
+     "C")

> require("longmemo")
Loading required package: longmemo

> fr <- .ffreq(500)

> B.1 <- B.specFGN(fr, H = 0.75, nsum = 200, k.approx = NA)

> B.xct <- B.specFGN(fr, H = 0.75, nsum = 10000, k.approx = NA)

> all.equal(B.xct, B.1)
[1] "Mean relative difference: 0.0001243095"

> fB <- function(x, lambda, H) {
+     u <- 2 * pi * x
+     h <- -(2 * H + 1)
+     (u + lambda)^h + (u - lambda)^h
+ }

> draw.f <- function(lambda, H, ..., log = "", ylim = if (any("y" == 
+     strsplit(log, "")[[1]])) NULL else c(0, 2 * fB1)) {
+     fB1 <- fB(1, lam .... [TRUNCATED] 

> op <- sfsmisc::mult.fig(4)$old.par

  When sourcing 'BspecFGN.R':
Error: there is no package called 'sfsmisc'
Execution halted

  'BspecFGN.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'BspecFGN.Rnw' using Sweave
Loading required package: longmemo

Error: processing vignette 'BspecFGN.Rnw' failed with diagnostics:
 chunk 4 (label = curve-fB) 
Error in loadNamespace(x) : there is no package called 'sfsmisc'

--- failed re-building 'BspecFGN.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'longmemo', 'partitions', 'fracdiff', 'mvtnorm',
  'RcppArmadillo'

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'dplyr', 'tidyr', 'ggplot2',
  'ggalluvial', 'FactoMineR', 'factoextra', 'lme4', 'purrr'

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

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

Packages suggested but not available for checking:
  'gee', '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: 'ggplot2', 'formula.tools'

Package suggested but not available for checking: 'rpart.plot'

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

Package suggested but not available for checking: 'tinytest'

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

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', '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: 'data.table', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 994 marked Latin-1 strings
Packages required but not available:
  'loon', 'ggplot2', 'ggmulti', 'gridExtra', 'scales', 'patchwork',
  'rlang'

Packages suggested but not available for checking:
  'GGally', 'magrittr', 'tidyr', 'zenplots', 'dplyr', 'gtable', 'png',
  'tibble', 'testthat', 'knitr', 'rmarkdown', 'covr', 'maps', 'hexbin',
  'nycflights13', 'ggplot2movies'

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

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

Packages suggested but not available for checking:
  'maps', 'sp', 'graph', 'scagnostics', 'PairViz', 'RColorBrewer',
  'loon.data', 'rworldmap', 'rgl', 'Rgraphviz', 'RDRToolbox',
  'kernlab', 'scales', 'testthat', 'knitr', 'rmarkdown', 'png',
  'formatR', '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:
  'loon', 'shiny', 'gridExtra', 'loon.ggplot', 'colourpicker',
  'base64enc'

Packages suggested but not available for checking:
  'magrittr', 'dplyr', 'ggmulti', 'testthat', 'knitr', 'rmarkdown',
  'tidyverse', 'covr', 'png'

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
fplot: no visible global function definition for 'rnorm'
fplot: no visible global function definition for 'segments'
fplot: no visible global function definition for 'points'
fplot: no visible global function definition for 'text'
fplot.foodweb: no visible global function definition for 'segments'
fplot.foodweb: no visible global function definition for 'points'
fplot.foodweb: no visible global function definition for 'text'
gplot: no visible global function definition for 'runif'
groupplot: no visible global function definition for 'rnorm'
groupplot: no visible global function definition for 'segments'
groupplot: no visible global function definition for 'points'
groupplot: no visible global function definition for 'text'
groupplot.foodweb: no visible global function definition for 'rnorm'
groupplot.foodweb: no visible global function definition for 'segments'
groupplot.foodweb: no visible global function definition for 'points'
groupplot.foodweb: no visible global function definition for 'text'
Undefined global functions or variables:
  points rnorm runif segments text
Consider adding
  importFrom("graphics", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available:
  'GenomicRanges', 'IRanges', 'S4Vectors'

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: 'checkmate', 'matrixStats'

Packages suggested but not available for checking:
  'bayesplot', 'brms', 'ggplot2', 'knitr', 'rmarkdown', 'rstan',
  'rstanarm', 'rstantools', 'spdep', 'testthat'

VignetteBuilder 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', 'futile.options', 'ggplot2', 'httr', 'dplyr', 'reshape2'

Packages suggested but not available for checking:
  'biomaRt', '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', 'Rcpp'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'clime', 'scio'
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'magrittr', 'emulator', 'tensor', 'magic'

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: 'magrittr', 'dineq'

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', 'rARPACK', 'svd'

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', 'shapes', 'e1071', 'pcaMethods', 'miscTools', 'rgl',
  'geomorph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'microbenchmark', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat) # nolint
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

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', 'RSQLite'

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: 'polynom', 'orthopolynom', 'Hmisc'

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

Package suggested but not available for checking: 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'scatterplot3d', 'dr'
Running examples in 'LPCM-Ex.R' failed
The error most likely occurred in:

> ### Name: gvessel
> ### Title: North Atlantic Water Temperature Data.
> ### Aliases: gvessel
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(gvessel)
> pairs(gvessel[,c(3,2,4,5)])
> tcol <- (gvessel$tempg- min(gvessel$tempg))/(max(gvessel$tempg)- min(gvessel$tempg))
> require(scatterplot3d)
Loading required package: scatterplot3d
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'scatterplot3d'
> scatterplot3d(gvessel[,2],gvessel[,4],gvessel[,5], color=rgb(tcol,0,1-tcol))
Error in scatterplot3d(gvessel[, 2], gvessel[, 4], gvessel[, 5], color = rgb(tcol,  : 
  could not find function "scatterplot3d"
Execution halted
Package required but not available: 'ggplot2'

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
lpint : <anonymous>: no visible global function definition for
  'integrate'
lpint: no visible global function definition for 'integrate'
lpint : lpint : <anonymous>: no visible global function definition for
  'integrate'
lplikint : lplikint.fun : <anonymous>: no visible global function
  definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Packages required but not available:
  'doParallel', 'dplyr', 'foreach', 'ggplot2', 'ggpubr', 'gridExtra',
  'lmtest', 'plm', 'sandwich', 'Rcpp', 'RcppArmadillo'

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

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

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

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

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

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

Package suggested but not available for checking: 'Rsymphony'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'BayesGOF', 'leaps', 'locfdr', 'Bolstad2', 'reshape2', 'ggplot2',
  'polynom', 'glmnet', 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'LPGraph', 'LPBkg', 'truncnorm', 'nloptr', 'Hmisc', 'orthopolynom',
  'polynom'

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

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: 'nleqslv'

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

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

Packages suggested but not available for checking: 'ald', 'qrLMM', 'qrNLMM'

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

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

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

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: 'mvtnorm'

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

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

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:
  'GeneticsPed', 'SparseM', 'quantreg', 'kinship2', 'MCMCglmm', 'rsvd',
  'R.matlab', 'sparsesvd'

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', 'rpact', 'mvtnorm', '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: 'wavethresh'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'LS2W', 'matrixStats', 'RandomFields', 'spdep'

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

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

Packages suggested but not available for checking:
  'BIFIEsurvey', 'TAM', 'miceadds', 'sirt', 'mice', 'pls', 'WrightMap',
  'irr', 'lavaan', 'difR', 'kerdiest', 'glmnet', 'mirt', 'car',
  'mitml', 'matrixStats', 'combinat', 'xtable', 'tensor', 'gtools',
  'plyr', 'prettyR', 'gridExtra'

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

Package suggested but not available for checking: 'tm'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'plyr', 'clue', 'gridExtra', 'reshape2', 'Rcpp',
  'mvtnorm', 'doParallel', 'foreach'

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

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

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

Package suggested but not available for checking: 'LSDsensitivity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'LSDinterface', 'tseries', 'kSamples', 'diptest', 'lawstat', 'abind',
  'sensitivity', 'car', 'randtoolbox', 'rgenoud', 'DiceKriging'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Lsdv.formula: no visible global function definition for 'model.frame'
Lsdv.formula: no visible global function definition for 'model.matrix'
Lsdv.formula: no visible global function definition for
  'model.response'
lsdv: no visible global function definition for 'pf'
summary.Lsdv: no visible global function definition for 'coef'
summary.Lsdv: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pf pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pf", "pt")
to your NAMESPACE file.
Package required but not available: 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
legend.lshorth: no visible global function definition for 'legend'
legend.lshorth: no visible global function definition for 'strwidth'
legend.lshorth: no visible global function definition for 'text'
plot.lshorth: no visible global function definition for 'plot.new'
plot.lshorth: no visible global function definition for 'plot.window'
plot.lshorth: no visible global function definition for 'axis'
plot.lshorth: no visible global function definition for 'title'
plot.lshorth: no visible global function definition for 'box'
plot.lshorth: no visible global function definition for 'lines'
plot.lshorth: no visible global function definition for 'legend'
plot.lshorth: no visible global function definition for 'strwidth'
plot.lshorth: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box legend lines plot.new plot.window strwidth text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot.new",
             "plot.window", "strwidth", "text", "title")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'MCMCpack', 'ggplot2', 'GPArotation', 'RcppArmadillo'

Package suggested but not available for checking: 'knitr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'R6', 'ggplot2', 'lavaan', 'RcppEigen'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'dplyr', 'scales', 'NFCP'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'ggplot2', 'pracma', 'combinat', 'matrixStats', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'seqinr', 'RCurl', 'data.table', 'bit64', 'R.utils'

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', 'scales', 'ggplot2', 'broom'

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: 'pls'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'raster', 'sp', 'rasterVis', 'latticeExtra', 'RColorBrewer'
'LazyData' is specified without a 'data' directory
Package required but not available: 'quantreg'

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

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

Package suggested but not available for checking: 'testthat'

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

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: 'waveslim', 'wavethresh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quanteda', 'quanteda.textstats', 'stringi', 'digest', 'RSpectra',
  'irlba', 'rsvd', 'rsparse', 'proxyC', 'ggplot2', 'ggrepel',
  'reshape2', 'locfit'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'coda', 'mcmcplots', 'ggmcmc', 'knitr', 'ggplot2', 'gridExtra',
  'reshape2'

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

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

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

Packages suggested but not available for checking:
  'SuperLearner', 'testthat', 'tmle', 'knitr', 'rmarkdown', 'nnls',
  'arm'

VignetteBuilder 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', 'polycor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
OC : Lnapprox: no visible global function definition for 'pnorm'
OC : Lnapprox: no visible global function definition for 'qnorm'
OC : Lt: no visible global function definition for 'pt'
OC : Lt: no visible global function definition for 'qnorm'
OC : OC_emwa2: no visible global function definition for 'pnorm'
OC : OC_emwa2: no visible global function definition for 'qnorm'
OC: no visible global function definition for 'pnorm'
OC: no visible global function definition for 'qnorm'
cmBE : LAtHy: no visible global function definition for 'phyper'
cmBE: no visible global function definition for 'uniroot'
planAOQL : Gderivacex: no visible global function definition for
  'pnorm'
planAOQL : Mnk: no visible global function definition for 'uniroot'
planAOQL : k0AOQL : delta: no visible global function definition for
  'pnorm'
planAOQL : alpha0: no visible global function definition for 'pnorm'
planAOQL : alpha0: no visible global function definition for 'qnorm'
planAOQL : fMSmodq2: no visible global function definition for
  'optimize'
planAOQL : kAOQL: no visible global function definition for 'uniroot'
planLTPD : nAPPROXL : k0L : g: no visible global function definition
  for 'qnorm'
planLTPD : nAPPROXL : k0L : h: no visible global function definition
  for 'qnorm'
planLTPD : nAPPROXL : k0L: no visible global function definition for
  'qnorm'
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  'pnorm'
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  'qnorm'
planLTPD : nAPPROXL: no visible global function definition for
  'uniroot'
planLTPD : kEWMA: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  optimize phyper pnorm pt qnorm uniroot
Consider adding
  importFrom("stats", "optimize", "phyper", "pnorm", "pt", "qnorm",
             "uniroot")
to your NAMESPACE file.
Packages required but not available: 'ipred', 'prodlim', 'partykit'

Packages suggested but not available for checking:
  'randomForestSRC', 'LTRCtrees'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'partykit', 'inum', 'icenReg', 'Icens', 'interval'

Packages suggested but not available for checking:
  'Formula', 'rpart.plot', '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: 'robustbase'

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

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

Packages suggested but not available for checking:
  'robustbase', 'rrcov', 'mvtnorm', '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: 'zoo'
Packages required but not available: 'generics', 'cpp11'

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

Packages which this enhances but not available for checking:
  'chron', 'timeDate', 'tis', '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: 'genetics'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'broom', 'dplyr', 'knitr', 'lme4', 'rjags', 'rmarkdown', 'sommer',
  '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:
  'mclust', 'networkD3', 'glasso', 'glmnet', 'jsonlite'

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:
  'Rcpp', 'fGarch', 'landpred', 'rootSolve', '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: 'raster', 'ncdf4'

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

Packages suggested but not available for checking:
  'caret', 'randomForest', 'gsubfn', 'Hmisc', 'plyr', 'RColorBrewer'

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

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bbmle', 'data.table', 'DEoptim', 'httr', 'lamW', 'matrixStats',
  'minpack.lm', 'mclust', 'plotrix', 'readxl', 'Rcpp', 'shape', 'XML',
  'zoo', 'RcppArmadillo'

Packages suggested but not available for checking:
  'spelling', 'plotly', 'rmarkdown', 'rstudioapi', 'rjags', 'coda',
  'pander', 'testthat', 'tiff', 'devtools', 'R.rsp'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
terrestrial.season: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'Rcpp', 'lubridate'

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

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

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

VignetteBuilder 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', 'magrittr', 'zeallot', 'rlang', 'coro', 'glue', 'progress',
  'R6', 'generics', 'purrr', 'ellipsis', 'fs', 'prettyunits', 'cli'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'Metrics', 'withr',
  'vdiffr', 'ggplot2', 'dplyr'

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

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

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ergm', 'network', 'igraph', 'ellipse', 'glmmML', 'mvtnorm',
  'corpcor'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'glue', 'purrr', 'rlang', 'rsample',
  'tibble', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'covr', 'devtools', 'forcats', 'fs', 'git2r', 'knitr', 'lme4',
  'rmarkdown', 'testthat', 'usethis', '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:
  'OpenMx', 'glasso', 'qgraph', 'psych', 'mvtnorm', 'corpcor', 'dplyr',
  'lavaan', 'semPlot'

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

Package suggested but not available for checking: 'depth'

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

Packages suggested but not available for checking:
  'magrittr', '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', 'vegperiod', 'foreach', 'iterators', 'doFuture',
  'future', 'progressr'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'ggplot2', 'plyr', 'gridExtra', 'gWQS', 'gamm4'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  lxb.c:62:25: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  lxb.c:62:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 4 [-Wformat-overflow=]
See 'C:/r_packages/pkgcheck/CRAN/lxb/lxb.Rcheck/00install.out' for details.
Packages required but not available: 'expm', 'corpcor'

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:
  'geosphere', 'caTools', 'ggplot2', 'randomForest', 'e1071', 'caret'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mpoly', 'stringr', 'memoise', 'gmp', 'usethis', 'Rcpp'

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

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ncdf4', 'rgdal', 'maps', 'mapdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GenomicRanges', 'GenomicAlignments', 'GenomicFeatures',
  'GenomeInfoDb', 'Rsamtools', 'IRanges'

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

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

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

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

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

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: 'C50'

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: 'lme4', 'optimx', 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'cli', 'dials', 'foreach', 'ggplot2', 'kernlab', 'magrittr',
  'party', 'polspline', 'progress', 'recipes', 'rlang', 'rsample',
  'Rsolnp', 'tibble'

Packages suggested but not available for checking:
  'adabag', 'BART', 'bartMachine', 'C50', 'doParallel', 'e1071',
  'earth', 'elasticnet', 'generics', 'gbm', 'glmnet', 'gridExtra',
  'Hmisc', 'kableExtra', 'kknn', 'knitr', 'lars', 'mboost', 'mda',
  'ParBayesianOptimization', 'parsnip', 'partykit', 'pls', 'pso',
  'randomForest', 'randomForestSRC', 'ranger', 'rBayesianOptimization',
  'rmarkdown', 'rms', 'testthat', 'tree', '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:
  'etl', 'dplyr', 'lubridate', 'readr', 'sf'

Packages suggested but not available for checking:
  'ggplot2', 'dbplyr', 'RSQLite', 'broom', 'knitr', 'leaflet', 'purrr',
  'rmarkdown', 'markdown', 'clifro', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BMA', 'plot.matrix', 'rlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pscl', 'sandwich', 'mediation', 'emplik', 'BB', 'mathjaxr'

Package suggested but not available for checking: 'SuppDists'

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

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: 'torch', '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: 'data.table', 'magrittr'

Packages suggested but not available for checking:
  'knitr', '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: 'matrixcalc', 'expm'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'lubridate', 'SharpeR', 'sandwich',
  'formatR', 'knitr'

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

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

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

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:
  'magclass', 'igraph', 'digest', 'stringi', 'yaml', 'withr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'tibble', 'ggplot2', '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:
  'metafor', 'R2wd', 'ggplot2'

Packages which this enhances but not available for checking:
  'compute.es', 'irr'
'library' or 'require' calls in package code:
  'R2wd' 'ggplot2' 'metafor'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'mrds'

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', 'geometry', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rmarkdown', 'knitr', 'ggplot2', 'TCGAbiolinks', 'maftools', 'DT',
  'htmltools', 'flexdashboard', 'bsplus', 'crosstalk', 'plotly',
  'canvasXpress', 'dplyr', 'ComplexHeatmap', 'circlize', 'ggbeeswarm',
  'ensurer', 'data.table', 'reshape2', 'GenomicRanges', 'IRanges',
  'pheatmap', 'tibble', 'readr', 'tidyr'

Package suggested but not available for checking: 'jsonlite'

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

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

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'reshape2', 'data.tree', 'raster',
  'ncdf4', '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', 'SeqArray', 'SeqVarTools', 'foreach', 'GMMAT',
  'CompQuadForm', 'RcppArmadillo'

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

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

Packages suggested but not available for checking: 'imager', 'fst'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'magick'

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

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

Packages suggested but not available for checking:
  'av', 'spelling', 'jsonlite', 'knitr', 'rmarkdown', 'rsvg', 'webp',
  'pdftools', 'ggplot2', 'gapminder', 'IRdisplay', 'tesseract',
  'gifski'

VignetteBuilder 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', 'tibble'

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

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

Packages suggested but not available for checking:
  'testthat', 'mvtnorm', '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: 'crul', 'jsonlite'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'coxme', 'doParallel', 'dplyr', 'foreach', 'iterators',
  'lme4', 'multcomp', 'plyr', 'qqman', 'seqinr'

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'data.table', 'tidyr', 'ggplot2', 'lpSolve', 'quadprog'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'commonmark', 'gmailr', 'rstudioapi', 'googledrive', 'rmarkdown',
  'glue', 'magrittr', 'purrr', 'fs', 'lifecycle', 'shiny', 'miniUI'

Packages suggested but not available for checking:
  'spelling', 'withr', 'covr', 'knitr', 'testthat', 'here', 'mockery',
  'readr'

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:
  'rJava', 'stringr', 'R.utils', 'assertthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'miscTools', 'robustbase', 'rrcov', 'pcaPP', 'mclust',
  'ggplot2', 'GGally', 'sn', 'withr', '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: 'jsonlite', 'urltools'

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

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

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

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', 'knitr', 'rmarkdown'

VignetteBuilder 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', 'RColorBrewer'

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

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

VignetteBuilder 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', 'R6', 'visNetwork'

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

Packages suggested but not available for checking:
  'curl', '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: 'AUC', 'grplasso'

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.
Package required but not available: 'e1071'

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

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

VignetteBuilder 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', 'curl', 'rgdal', 'raster', 'sp', 'xml2', 'gridExtra',
  'httr', 'dplyr', 'stringi', 'tidyr', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'palettetown', 'magrittr',
  'tibble', 'rdhs'

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

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

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:
  'MALDIquant', 'base64enc', 'digest', 'readBrukerFlexData',
  'readMzXmlData', 'XML'

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

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/MALDIquantForeign-intro.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', 'testthat'

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

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/MALDIquant-intro.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/MALDIquant-intro.Rnw'
(Is a VignetteBuilder field missing?)
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'MALDIquant', 'signal', 'robustbase', 'waveslim'

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: 'rJava'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'reshape2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'msma', 'oro.nifti', 'oro.dicom', 'imager', 'caret'

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

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

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kinship2'
Error(s) in re-building vignettes:
--- re-building 'Mangrove.Rnw' using Sweave

Error: processing vignette 'Mangrove.Rnw' failed with diagnostics:
 chunk 19 
Error in library(kinship2) : there is no package called 'kinship2'

--- failed re-building 'Mangrove.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'magrittr', 'plotly', 'ggplot2'

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:
  'reshape2', 'ggplot2', 'ggrepel', 'gridExtra'

Packages suggested but not available for checking: 'R.utils', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'NLP', 'tm', 'magrittr', 'httr', 'jsonlite', 'functional', 'zoo',
  'psych', 'base64enc', 'htmlwidgets', 'DT', 'htmltools', 'purrr',
  'readr', 'dplyr', 'tidyselect', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'R.rsp', 'haven', 'readxl',
  'devtools', 'formatR', 'highr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', '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:
  'shiny', 'miniUI', 'htmltools', 'htmlwidgets', 'knitr', 'base64enc',
  'webshot', 'shinyjs'

Packages suggested but not available for checking:
  'dygraphs', 'leaflet', 'plotly', 'xts', '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: 'locfit', 'scales', 'statmod'

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

VignetteBuilder 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', 'magic', 'plotrix', 'ellipse', 'multcomp', 'data.table'

Packages suggested but not available for checking:
  'RGtk2', 'knitr', 'rmarkdown', 'HSAUR3', 'tidyr', 'ggplot2', 'GFD',
  '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:
  'caret', 'Metrics', 'e1071', 'dplyr', 'ggplot2', 'lme4'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', '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:
  'reticulate', 'nsga2R', 'lhs', 'stringr', 'randtoolbox', 'e1071',
  'gtools', '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:
  'Rcpp', 'Rdpack', 'RSpectra', 'Rtsne', 'RANN', 'labdsv', 'shapes',
  'fastcluster', 'dbscan', 'RcppArmadillo', 'RcppDist'

Package suggested but not available for checking: 'igraph'

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

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

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

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

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', 'sf', 'jsonlite', 'purrr', 'curl', 'dplyr', 'tidyr',
  'aws.s3', 'stringi', 'slippymath', 'protolite', 'rlang', 'geojsonsf',
  'magick', 'leaflet', 'units', 'raster', 'png', 'jpeg'

Packages suggested but not available for checking:
  'mapdeck', 'tigris', 'tidycensus', 'tmap', 'ggspatial'

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

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: 'dplyr', 'ggplot2', 'magrittr'

Package suggested but not available for checking: 'knitr'

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

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

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'RColorBrewer', 'showtext'

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

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

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

VignetteBuilder 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', 'MANOVA.RM', 'shiny', 'shinydashboardPlus', 'shinydashboard',
  'MultBiplotR', 'broom', 'car', 'dplyr', 'highcharter', 'htmltools',
  'nortest', 'purrr', 'reshape', 'shinycssloaders', 'stringr',
  'tibble', 'MVN', 'heplots', 'mvnormtest', 'vegan', 'waiter',
  'moments', 'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'BH',
  'RcppEigen', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'htmltools', 'htmlwidgets', 'jsonlite', 'leafem', 'leaflet',
  'leaflet.extras', 'leafpm', 'mapview', 'miniUI', 'raster', 'scales',
  'sf', 'shiny', 'sp'

Package suggested but not available for checking: 'crayon'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cf1.sample: no visible global function definition for 'rexp'
cf1.sample: no visible global function definition for 'rmultinom'
dherlang : <anonymous> : <anonymous>: no visible global function
  definition for 'dgamma'
erhmm.param.kmeans: no visible global function definition for 'kmeans'
erhmm.param.kmeans: no visible global function definition for 'var'
erhmm.param.kmeans: no visible global function definition for 'runif'
gmmpp.param.kmeans: no visible global function definition for 'kmeans'
gmmpp.param.kmeans: no visible global function definition for 'runif'
herlang.param.kmeans: no visible global function definition for
  'kmeans'
herlang.param.kmeans: no visible global function definition for 'var'
map.param.kmeans: no visible global function definition for 'kmeans'
map.param.kmeans: no visible global function definition for 'runif'
ph.param.random: no visible global function definition for 'runif'
ph.sample: no visible global function definition for 'rmultinom'
ph.sample: no visible global function definition for 'rexp'
pherlang : <anonymous> : <anonymous>: no visible global function
  definition for 'pgamma'
rherlang: no visible global function definition for 'rmultinom'
rherlang : <anonymous>: no visible global function definition for
  'rgamma'
Undefined global functions or variables:
  dgamma kmeans pgamma rexp rgamma rmultinom runif var
Consider adding
  importFrom("stats", "dgamma", "kmeans", "pgamma", "rexp", "rgamma",
             "rmultinom", "runif", "var")
to your NAMESPACE file.
Packages required but not available: 'sp', 'gam', 'maptools', 'colorspace'

Packages suggested but not available for checking:
  'maps', 'mapproj', 'PBSmapping'

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

Packages suggested but not available for checking:
  'EcoHydRology', 'geosphere'

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

Packages suggested but not available for checking:
  'ggplot2', 'latticeExtra', 'sp', 'progress'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spruce', 'Seurat', 'dbarts', 'ggplot2', 'dplyr', 'ggalluvial',
  'plotly', 'shiny', 'rlang'

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:
  'RColorBrewer', 'classInt', 'rgdal', 'rgeos', 'geosphere', 'knitr',
  'markdown'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tmap', 'cartography', 'ggplot2', 'rgdal', 'sf', 'dplyr', 'leaflet',
  'tmaptools', 'viridisLite', 'httr', 'curl', 'htmltools', 'leafpop',
  'leafsync', 'mapview', 'geojsonio', 'jsonlite', 'stringr', 's2',
  'stringi'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: 'shapefiles'
Package unavailable to check Rd xrefs: 'shapefiles'
Running examples in 'mapplots-Ex.R' failed
The error most likely occurred in:

> ### Name: draw.shape
> ### Title: Draw shapefiles in an existing plot
> ### Aliases: draw.shape
> 
> ### ** Examples
> 
> library(shapefiles)
Error in library(shapefiles) : there is no package called 'shapefiles'
Execution halted
Packages required but not available:
  'Rcpp', 'RcppParallel', 'RCurl', 'fields', 'ggpubr', 'ggsci',
  'rstudioapi', 'scatterplot3d', 'dplyr', 'crayon', 'cli', 'magrittr',
  'reshape2', 'ggplot2', 'smacof', 'princurve', 'dendextend', 'vcfR',
  'zoo', 'plotly'

Packages suggested but not available for checking:
  'testthat', 'updog', 'fitPoly', 'polymapR', 'AGHmatrix',
  'gatepoints', 'knitr', 'rmarkdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'memoise', 'progress', 'pbmcapply', 'parallelly', 'purrr', 'rlang'

Package suggested but not available for checking: 'testthat'

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

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

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', 'rgdal', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'leaflet', 'spocc', 'sp', 'maps', 'RColorBrewer',
  'jsonlite', 'gistr', 'data.table'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'taxize', 'maptools', 'rgbif', 'scrubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'sf', 'bitops', 'stars', 'RgoogleMaps', 'httr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'curl', 'fs', 'glue', 'magick', 'magrittr', 'memoise',
  'pdftools', 'png', 'purrr', 'raster', 'Rcpp', 'reproj', 'RNiftyReg',
  'sf', 'slippymath', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'gibble', 'jpeg', 'knitr', 'lwgeom', 'mapview',
  'mmand', 'osmdata', 'polyclip', 'rmarkdown', 'spelling', '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:
  'knitr', 'ggplot2', 'dplyr', 'sf'
Note: found 996 marked UTF-8 strings
Packages required but not available: 'sf', 'classInt', 'Rcpp'

Packages suggested but not available for checking:
  'terra', 'png', 'jpeg', 'lwgeom', 'knitr', 'rmarkdown', 'tinytest',
  'covr'

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

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

Packages suggested but not available for checking:
  'ggplot2', 'ggspatial', 'knitr', 'leaflet', 'png', 'raster',
  'rmarkdown', 'slippymath', 'terra', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'mapproj', 'mapdata', 'sp', 'rnaturalearth'
Packages unavailable to check Rd xrefs: 'sp', 'rgdal', 'mapproj'
Packages required but not available:
  'raster', 'gstat', 'rgdal', 'sp', 'rgeos'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'survey', 'maptools', 'RColorBrewer', 'Hmisc', 'classInt', 'sp',
  'colorspace', 'reshape2'

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

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

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

Packages suggested but not available for checking:
  'rgeos', 'spatstat.geom', 'PBSmapping', 'maps', 'RColorBrewer',
  'raster', 'polyclip', 'plotrix', 'spatstat.linnet', 'spatstat.utils',
  'spatstat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'htmltools', 'htmlwidgets', 'leafem', 'leaflet',
  'leafpop', 'png', 'raster', 'satellite', 'scales', 'servr', 'sf',
  'sp', 'webshot'

Packages suggested but not available for checking:
  'covr', 'knitr', 'later', 'leaflet.extras2', 'leafsync', 'lwgeom',
  'mapdeck', 'plainview', 'poorman', 'rmarkdown', 'rstudioapi', 's2',
  'stars', 'tinytest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'mvtnorm', 'RColorBrewer', 'minpack.lm', 'zoo', 'numDeriv',
  'magrittr', 'scales'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tkrplot'
Packages required but not available:
  'readr', 'rlang', 'dplyr', 'usethis', 'devtools', 'SnowballC',
  'lubridate', 'rvest', 'scholar', 'purrr', 'stringi', 'stringr',
  'tidytext', 'tidyr', 'tidyverse', 'treemapify', 'tibble', 'widyr',
  'writexl', 'igraph'

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

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

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

Packages suggested but not available for checking:
  'bench', 'brms', 'broom', 'data.table', 'dplyr', 'emmeans', 'ggdist',
  'ggplot2', 'ggbeeswarm', 'gt', 'haven', 'kableExtra', 'knitr',
  'magrittr', 'margins', 'modelsummary', 'systemfonts', 'patchwork',
  'quantreg', 'rlang', 'rmarkdown', 'testthat', 'tidyverse', 'vdiffr',
  'AER', 'aod', 'betareg', 'bife', 'brglm2', 'crch', 'estimatr',
  'fixest', 'gam', 'geepack', 'glmx', 'ivreg', 'lme4', 'lmerTest',
  'mclogit', 'ordinal', 'plm', 'pscl', 'rms', 'robust', 'robustbase',
  'robustlmm', 'rstantools', 'rstanarm', 'sandwich', 'scam',
  'speedglm', 'survey', 'truncreg', 'covr', 'spelling'

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

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

VignetteBuilder package required for checking but not installed: 'R.rsp'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'magrittr', 'cli', 'crayon', 'rstudioapi', 'purrr', 'tibble',
  'furniture', 'betareg', 'stringr'

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

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

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

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'gapminder', 'sandwich',
  'stargazer', 'lme4'

Packages which this enhances but not available for checking:
  'AER', 'betareg', 'ordinal', 'survey'

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

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

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

Packages suggested but not available for checking:
  'cond', 'csampling', 'nlreg'

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

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

Packages suggested but not available for checking: 'knitr', '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:
  'lme4', 'R2admb', 'truncnorm', 'coda', 'numDeriv', 'expm', 'Rcpp',
  'TMB', 'optimx', 'data.table', 'knitr', 'kableExtra', 'bookdown'

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: 'Rcpp', 'RSpectra', 'RcppEigen'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'iterators', 'doParallel', 'foreach', 'reshape2',
  'CausalImpact', 'tidyr', 'zoo', 'bsts', 'scales', 'Boom', 'utf8',
  'dtw'

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

VignetteBuilder 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', 'tidyr', 'tibble'

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

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

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

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:
  'Rcpp', 'ape', 'numDeriv', 'phangorn', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', '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:
  'igraph', 'matlab', 'expm', 'Rcpp', 'RcppParallel', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'diagram', 'DiagrammeR', 'msm', 'Rsolnp',
  'rmarkdown', 'ctmcd', 'bookdown', 'rticles'

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

VignetteBuilder 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', 'optimParallel', 'foreach', 'ggplot2', 'metR'

Packages suggested but not available for checking:
  'knitr', 'kableExtra', 'gridExtra', 'reshape2', '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: 'survidm', 'mstate'

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

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

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

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

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

Packages suggested but not available for checking:
  'bench', 'bib2df', 'crayon', 'covr', 'desc', 'dplyr', 'haven',
  'knitr', 'rcmdcheck', 'stringi', 'spelling', 'testthat', 'tibble',
  'waldo', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
negbin.rel.clust: no visible global function definition for 'kmeans'
negbin.rel.clust: no visible global function definition for 'matplot'
negbin.rel.pca: no visible global function definition for 'princomp'
negbin.rel.pca: no visible global function definition for 'biplot'
pois.rel.clust: no visible global function definition for 'kmeans'
pois.rel.clust: no visible global function definition for 'matplot'
pois.rel.pca: no visible global function definition for 'princomp'
pois.rel.pca: no visible global function definition for 'biplot'
sim.negbin: no visible global function definition for 'rnbinom'
sim.pois: no visible global function definition for 'rpois'
wt.rel.negbin: no visible global function definition for 'var'
wt.rel.negbin: no visible global function definition for 'optimize'
wt.rel.negbin: no visible global function definition for 'integrate'
wt.rel.pois: no visible global function definition for 'optimize'
wt.rel.pois: no visible global function definition for 'integrate'
Undefined global functions or variables:
  biplot integrate kmeans matplot optimize princomp rnbinom rpois var
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "biplot", "integrate", "kmeans", "optimize",
             "princomp", "rnbinom", "rpois", "var")
to your NAMESPACE file.
Packages required but not available:
  'DBI', 'RSQLite', 'gdistance', 'geosphere', 'sp', 'raster', 'ncdf4',
  'plotrix', 'shape', 'reshape2', 'adehabitatMA', 'ggplot2'

Packages suggested but not available for checking:
  'maps', 'mapdata', 'mapproj', '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: 'doParallel', 'foreach'

Packages suggested but not available for checking:
  'microbenchmark', 'knitr', 'rmarkdown', 'rticles', 'ggplot2',
  'viridis', 'patchwork', 'xtable'

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 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
mAr.pca: no visible binding for global variable 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Packages required but not available: 'neuralnet', 'earth'

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

Packages suggested but not available for checking:
  'broom', 'forecast', 'Formula', 'ggplot2', 'gridExtra', 'Hmisc',
  'lme4', 'maps', 'stringr', 'tidyr', 'xtable', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'devtools', 'forestinventory', 'JoSAE', 'knitr', 'microbenchmark',
  'pkgload', 'rmarkdown', 'rprojroot', 'rsae', 'RUnit', 'R.rsp', 'sae',
  'testthat'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'
Packages unavailable to check Rd xrefs: 'sae', 'rsae', 'JoSAE', 'forestinventory'
Running 'runit.R'
Running the tests in 'tests/runit.R' failed.
Complete output:
  > #!/usr/bin/Rscript --vanilla
  > is_failure <- function(result) {
  +     res <- RUnit::getErrors(result)
  +     names(res) <- tolower(names(res)) # soothe lintr
  +     sum_of_exceptions <- res[["nerr"]] + res[["nfail"]]
  +     fail <- as.logical(sum_of_exceptions)
  +     return(fail)
  + }
  > 
  > if (interactive()) {
  +     pkgload::load_all(path = ".") # needed to use pkgload's shim version of
  +     # base's system.file
  +     unit_dir <- system.file("inst", "runit_tests", package = "maSAE")
  + } else {
  +     require("maSAE", quietly = TRUE, character.only = TRUE) ||
  +         pkgload::load_all(path = ".") # needed to use pkgload's shim version of
  +     r_call <- commandArgs(trailingOnly = FALSE)
  +     if (any(grepl("--file", r_call))) {
  +         unit_dir <- file.path("inst", "runit_tests")
  +     } else {
  +         unit_dir <- system.file("runit_tests", package = "maSAE")
  +     }
  + }
  
  Attaching package: 'maSAE'
  
  The following object is masked from 'package:stats':
  
      predict
  
  > if (! dir.exists(unit_dir)) {
  +     stop("Can not find RUnit test directory ", unit_dir,
  +          ". Try to (re)install the package first.")
  + }
  > setup_file <- file.path(unit_dir, "setup.R")
  > if (file.exists(setup_file)) source(setup_file)
  > package_suite <- RUnit::defineTestSuite("maSAE_unit_test",
  +                                         dirs = unit_dir,
  +                                         testFileRegexp = "^runit.*\\.[rR]",
  +                                         testFuncRegexp = "^test_+")
  Error in loadNamespace(x) : there is no package called 'RUnit'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Errors in running code in vignettes:
when running code in 'maSAE.Rnw'
Error in loadVignetteBuilder(pkgdir) : vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  'maSAE.Rnw' using 'UTF-8'... failed to complete the test
Packages required but not available:
  'glmnet', 'survey', 'dplyr', 'magrittr', 'rpms', 'Rdpack'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ashr', 'assertthat', 'plyr', 'rmeta', 'Rcpp', 'mvtnorm', 'abind',
  'softImpute', 'RcppArmadillo', 'RcppGSL'

Packages suggested but not available for checking:
  'REBayes', 'corrplot', 'testthat', 'kableExtra', 'knitr',
  'rmarkdown', 'profmem', 'flashr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gdalUtils', 'dismo', 'dplyr', 'e1071', 'lubridate', 'magrittr',
  'maptools', 'raster', 'rgdal', 'sp', 'tidyverse', 'virtualspecies'

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

VignetteBuilder 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', 'magrittr', 'purrr', 'rlang', 'tibble', 'tidyr',
  'tidyselect'

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

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

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

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: 'demoKde'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'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
Note: found 1 marked UTF-8 string
Packages required but not available:
  'coda', 'genetics', 'gtools', 'kinship2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RANN', 'corrplot', 'xtable', 'repmis', '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:
  'rstudioapi', 'tibble', 'readr', 'jsonlite', 'clipr', 'purrr',
  '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:
  'ggplot2', 'mvnfast', 'rcbalance', 'Rcpp'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'mvtnorm', 'optmatch', 'RItools', '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', 'httr', 'jsonlite'
Packages required but not available:
  'Rcpp', 'RcppProgress', 'rJava', 'lpSolve', 'partitions',
  'RcppArmadillo'

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

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

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

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

> ### Name: GenMatch
> ### Title: Genetic Matching
> ### Aliases: GenMatch
> ### Keywords: nonparametric
> 
> ### ** Examples
> 
> data(lalonde)
> attach(lalonde)
> 
> #The covariates we want to match on
> X = cbind(age, educ, black, hisp, married, nodegr, u74, u75, re75, re74)
> 
> #The covariates we want to obtain balance on
> BalanceMat <- cbind(age, educ, black, hisp, married, nodegr, u74, u75, re75, re74,
+                     I(re74*re75))
> 
> #
> #Let's call GenMatch() to find the optimal weight to give each
> #covariate in 'X' so as we have achieved balance on the covariates in
> #'BalanceMat'. This is only an example so we want GenMatch to be quick
> #so the population size has been set to be only 16 via the 'pop.size'
> #option. This is *WAY* too small for actual problems.
> #For details see http://sekhon.berkeley.edu/papers/MatchingJSS.pdf.
> #
> genout <- GenMatch(Tr=treat, X=X, BalanceMatrix=BalanceMat, estimand="ATE", M=1,
+                    pop.size=16, max.generations=10, wait.generations=1)
Loading required namespace: rgenoud
Failed with error:  'there is no package called 'rgenoud''
Error in loadNamespace(x) : there is no package called 'rgenoud'
Calls: GenMatch ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'AbadieImbens.R'
  Comparing 'AbadieImbens.Rout' to 'AbadieImbens.Rout.save' ... OK
  Running 'DehejiaWahba.R'
  Comparing 'DehejiaWahba.Rout' to 'DehejiaWahba.Rout.save' ... OK
  Running 'GenMatch.R'
Running the tests in 'tests/GenMatch.R' failed.
Complete output:
  > suppressMessages(library(rgenoud))
  Error in library(rgenoud) : there is no package called 'rgenoud'
  Calls: suppressMessages -> withCallingHandlers -> library
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

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

Packages suggested but not available for checking:
  'optmatch', 'Matching', 'rgenoud', 'CBPS', 'dbarts', 'randomForest',
  'glmnet', 'gbm', 'cobalt', 'lmtest', 'sandwich', 'RcppProgress',
  'Rglpk', 'Rsymphony', 'gurobi', 'knitr', 'rmarkdown'

VignetteBuilder 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', 'Matching'

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

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: 'rlang'

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

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

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

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

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'jpeg', 'magrittr', 'png', 'readbitmap', 'stringr', 'downloader',
  'imager', 'moments'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'js'
Packages required but not available:
  'purrr', 'base64enc', 'httr', 'rstudioapi', 'texPreview', 'magick'

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:
  'dfoptim', 'mvtnorm', 'seriation', 'igraph', 'gplots', 'cba'

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
Malformed Description field: should contain one or more complete sentences.
Found the following possibly unsafe calls:
File 'matlab/R/zzz.R':
  unlockBinding("savedTime", .MatlabNamespaceEnv)

colorbar : colorbar.EO: no visible global function definition for 'par'
colorbar : colorbar.EO: no visible global function definition for
  'axis'
colorbar : colorbar.EO: no visible global function definition for
  'axTicks'
colorbar : colorbar.EO: no visible global function definition for 'box'
colorbar : colorbar.NO: no visible global function definition for
  'axis'
colorbar : colorbar.NO: no visible global function definition for
  'axTicks'
colorbar : colorbar.NO: no visible global function definition for 'box'
imagesc : pretty.axp: no visible global function definition for 'par'
imagesc: no visible global function definition for 'axis'
imagesc: no visible global function definition for 'box'
jet.colors: no visible global function definition for 'rgb'
multiline.plot.colors : get.gca.colororder: no visible global function
  definition for 'rgb'
std: no visible global function definition for 'sd'
Undefined global functions or variables:
  axTicks axis box par rgb sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axTicks", "axis", "box", "par")
  importFrom("stats", "sd")
to your NAMESPACE file.
Package required but not available: 'stringr'

Package suggested but not available for checking: 'covr'

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

Packages suggested but not available for checking:
  'knitr', 'rglwidget', 'rmarkdown', 'carData', 'webshot2', '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:
  'shiny', 'data.table', 'dplyr', 'tidyr', 'tidyselect', 'plotly',
  'DT', 'shinydashboard', 'shinyWidgets', 'forecast', 'parsedate',
  'lubridate'

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

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

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', 'plotrix', 'pracma', 'progress', 'RSpectra', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RhpcBLASctl', 'float'

Packages suggested but not available for checking:
  'testthat', 'data.table', '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: 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'plyr', 'glasso', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doSNOW', 'foreach', 'snow', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

Packages suggested but not available for checking:
  'formatR', 'knitr', 'LaplacesDemon', 'matrixcalc', 'matrixsampling',
  'MBSP', 'rmarkdown', 'roxygen2', 'sessioninfo', 'spelling',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertive', 'matrixcalc', 'lavaan', 'psych'

Packages suggested but not available for checking:
  'simsem', 'RUnit', 'semPLS', 'ASGSCA', 'knitr', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'TTR', 'zoo', 'fftw', 'signal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'Rcpp', 'RcppParallel', 'RcppProgress', 'RcppThread'

Packages suggested but not available for checking:
  'testthat', 'debugme', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'expm'

Packages which this enhances but not available for checking:
  'MatrixModels', 'graph', 'SparseM', 'sfsmisc', 'igraph', 'maptools',
  'sp', 'spdep'
Packages unavailable to check Rd xrefs: 'SparseM', 'spdep', 'expm', 'graph', 'igraph', 'sfsmisc', 'MatrixModels', 'maptools', 'sp'
Package required but not available: 'keep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'base64enc', 'ggplot2', 'knitr', 'markdown', 'microbenchmark',
  'R.devices', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Packages suggested but not available for checking: 'ggplot2', 'reshape2'
Package required but not available: 'matrixStats'

Packages suggested but not available for checking:
  'testthat', 'moments', 'car', 'cosinor', 'cosinor2', 'PMCMRplus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'grr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MGRASTer', 'BIOM.utils'

Packages suggested but not available for checking:
  'RJSONIO', 'qvalue', 'ecodist', 'gplots', 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'dplyr', 'Hmisc', 'magrittr', 'purrr', 'rlang',
  'stringi', 'tibble'

Packages suggested but not available for checking:
  'covr', 'knitr', 'matsindf', '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:
  'dplyr', 'magrittr', 'matsbyname', 'purrr', 'rlang', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'knitr', 'RCLabels', '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: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'tidyr', 'magrittr', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'gtools', 'stringr', 'igraph', 'RColorBrewer',
  'ggplot2', '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: 'beastier', 'stringr'

Packages suggested but not available for checking:
  'beautier', 'curl', 'knitr', 'markdown', 'rmarkdown', 'testit',
  'testthat'

VignetteBuilder 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', 'mda', 'RcppArmadillo'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'corpcor', 'foreach', 'multcomp', 'randomForest'

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: 'aucm', 'Rsolnp', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'purrr', 'rlang', 'mstate', 'MCMCpack', 'dplyr',
  'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'raster'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CVXR', 'glmnet', 'intervals', 'SIHR'

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: 'plgp'

Package suggested but not available for checking: 'lhs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'raster'

Package suggested but not available for checking: 'dismo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'miscTools', 'sandwich', 'generics'

Packages suggested but not available for checking:
  'clue', 'dlm', 'plot3D', 'tibble', 'tinytest'

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: 'GenSA', 'pso', 'GA', 'NMOF', 'scales'

Packages suggested but not available for checking:
  'fUnitRoots', 'microbenchmark', 'knitr', 'rmarkdown'

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.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'exactRankTests', 'mvtnorm'

Package suggested but not available for checking: 'TH.data'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'aucm', 'Rsolnp'

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', 'quickcheck', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'digest', 'dplyr', 'futile.logger', 'lubridate',
  'magrittr', 'purrr', 'rlang', 'rvest', 'stringr', 'tibble', 'xml2'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'testthat', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'geodist', 'httr', 'jsonlite', 'leaflet', 'lubridate',
  'magrittr', 'MazamaCoreUtils', 'MazamaSpatialUtils', 'readr',
  'rlang', 'stringr', 'tidygeocoder'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'testthat', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'rmarkdown', 'roxygen2', 'testthat', 'zoo'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MazamaSpatialUtils', 'dplyr', 'magrittr', 'MazamaCoreUtils',
  'rlang', 'sp', 'sf', 'tmap'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'testthat', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'cleangeo', 'countrycode', 'dplyr', 'magrittr',
  'MazamaCoreUtils', 'rgdal', 'rgeos', 'rlang', 'rmapshaper', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'maps', 'markdown', 'readr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'geodist', 'lubridate', 'magrittr', 'MazamaCoreUtils',
  'readr', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'testthat', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TurtleGraphics'

Packages suggested but not available for checking: 'testthat', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'foreach'

Packages suggested but not available for checking:
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VignetteBuilder packages required for checking but not installed:
  'R.rsp', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rmarkdown', 'emojifont', 'knitr', 'markdown', 'png', 'testthat',
  'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BH'

Package suggested but not available for checking: 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mclust', 'Rmixmod', 'mvtnorm'

Packages suggested but not available for checking: 'network', 'jpeg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
MI.2: no visible global function definition for 'xtabs'
RNASeq.Data: no visible binding for global variable 'quantile'
loc.node: no visible global function definition for 'head'
loc.node: no visible global function definition for 'tail'
plotHybrid.Tree: no visible global function definition for 'par'
plotHybrid.Tree: no visible global function definition for 'text'
plotHybrid.Tree: no visible global function definition for 'image'
plotHybrid.Tree: no visible global function definition for 'grey'
plotHybrid.Tree: no visible global function definition for
  'heat.colors'
plotHybrid.Tree: no visible global function definition for 'head'
plotHybrid.Tree: no visible global function definition for 'segments'
plotbr: no visible global function definition for 'segments'
Undefined global functions or variables:
  grey head heat.colors image par quantile segments tail text xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Packages required but not available:
  'ade4', 'doParallel', 'foreach', 'kknn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'energy', 'FNN'

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:
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Package suggested but not available for checking: 'gsl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'bigmemory', 'foreach', 'lme4', 'logging'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geometry', 'randtoolbox', 'mvtnorm', 'raster'

Packages suggested but not available for checking:
  'fields', 'knitr', 'spsurvey'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/MBHdesign.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
cfull: no visible global function definition for 'combn'
cl: no visible global function definition for 'combn'
cn: no visible global function definition for 'combn'
crep: no visible global function definition for 'combn'
crich: no visible global function definition for 'combn'
ct: no visible global function definition for 'combn'
mjaccard: no visible global function definition for 'combn'
ml: no visible global function definition for 'combn'
mn: no visible global function definition for 'combn'
mrep: no visible global function definition for 'combn'
mrich: no visible global function definition for 'combn'
msorensen: no visible global function definition for 'combn'
mt: no visible global function definition for 'combn'
wnodf: 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: 'effsize', 'psych'

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: 'robustbase', 'chipPCR'

Packages suggested but not available for checking:
  'spelling', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'devtools', 'roxygen2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'scales', 'dplyr', 'R2jags', 'rjags', 'magrittr', 'checkmate',
  'Rdpack', 'igraph', 'rgeos', 'reshape2'

Packages suggested but not available for checking:
  'overlapping', 'ggplot2', 'RColorBrewer', 'mcmcplots', 'coda',
  'testthat', 'crayon', 'forestplot', 'ggdist', 'lspline', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'dplyr', 'R2jags', 'rjags', 'reshape2', 'magrittr',
  'checkmate', 'Rdpack'

Packages suggested but not available for checking:
  'scales', 'overlapping', 'ggplot2', 'ggdist', 'igraph', 'rgeos',
  'crayon', 'Hmisc', 'lspline', 'rmarkdown', 'zoo', 'testthat',
  'RColorBrewer', 'mcmcplots'

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:
  'stabs', 'nnls', 'quadprog', 'partykit'

Packages suggested but not available for checking:
  'TH.data', 'fields', 'BayesX', 'gbm', 'mlbench', 'RColorBrewer',
  'randomForest', 'testthat', 'kangar00'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reticulate', 'tibble', 'magrittr', 'purrr', 'dplyr', 'lubridate',
  'stringr', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'data.table', 'dplyr', 'forcats', 'ggforce', 'ggplot2',
  'magrittr', 'purrr', 'rlang', 'tidyr', 'tibble'

Package suggested but not available for checking: 'RProbSup'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nleqslv', 'enrichwith'

Package suggested but not available for checking: 'brglm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'dplR', 'Rfast'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MCMCpack', 'mnormt', 'truncnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GIGrvg', 'coda', 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'KFAS', 'pscl', 'MCMCpack', 'ggplot2', 'reshape2', 'BBmisc',
  'matrixStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

Packages suggested but not available for checking:
  'fitdistrplus', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RNetCDF'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggrepel', 'gridExtra', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'backports', 'checkmate', 'data.table', 'mlr3', 'mlr3misc',
  'mlr3pipelines', 'mlr3proba', 'R6', 'glmnet'

Packages suggested but not available for checking:
  'curl', 'lgr', 'formattable', 'tidyverse', 'PracTools',
  'mlr3learners', 'mlr3oml', 'neuralnet', 'paradox', 'testthat',
  'knitr', 'ranger', 'rmarkdown', 'xgboost', '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:
  'leaps', 'lars', 'glmnet', 'ncvreg', 'smoothmest', 'ggplot2',
  'reshape2'

Packages suggested but not available for checking: 'flare', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'e1071', 'pROC', 'caret', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dummies', 'magic', 'stringr', 'ggplot2', 'wordcloud', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ROCR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lpSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getbetap.A: no visible global function definition for 'pbeta'
getbetap.A: no visible global function definition for 'cor.test'
Undefined global functions or variables:
  cor.test pbeta
Consider adding
  importFrom("stats", "cor.test", "pbeta")
to your NAMESPACE file.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rglpk', 'glpkAPI', 'RColorBrewer', 'combinat'

Packages suggested but not available for checking: 'Rgraphviz', 'cplexAPI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RankAggreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'trust', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'flexclust', 'faraway'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GA', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'assertthat', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'mvtnorm', 'tweedie', '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: 'randtoolbox', 'snow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gridBase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'metafor', 'boot.heterogeneity'

Packages suggested but not available for checking:
  'HSAUR3', 'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 46 marked UTF-8 strings
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: 'statmod', 'locfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'memisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'expm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mclust', 'foreach', 'iterators', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'doParallel', 'doRNG', 'cli', 'crayon', 'knitr', 'rmarkdown'

VignetteBuilder 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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mix', 'geometry'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'evir'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'chk', 'extras', 'mcmcr', 'nlist', 'purrr', 'universals'

Packages suggested but not available for checking:
  'coda', 'covr', 'doParallel', 'plyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'future.apply', 'progressr'

Packages suggested but not available for checking:
  'bayesplot', 'coda', 'mockery', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'ape', 'corpcor', 'tensorA', 'cubature'

Packages suggested but not available for checking:
  'rgl', 'combinat', 'mvtnorm', 'orthopolynom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MCMCglmm', 'ggplot2', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'HDInterval', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coda', 'mcmc', 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'sfsmisc', 'colorspace', 'denstrip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'combinat', 'RcppArmadillo', 'RcppProgress', 'RcppEigen'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MCMCglmm', 'ggplot2', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'xtable', 'Iso'
Running 'accept-batch.R'
  Comparing 'accept-batch.Rout' to 'accept-batch.Rout.save' ... OK
  Running 'circle.R'
  Comparing 'circle.Rout' to 'circle.Rout.save' ...9,11d8
< Warning message:
< In RNGkind("Marsaglia-Multicarry") :
<   RNGkind: Marsaglia-Multicarry has poor statistical properties
  Running 'initseq.R'
Running the tests in 'tests/initseq.R' failed.
Complete output:
  > 
  >  library(mcmc)
  > 
  >  set.seed(42)
  > 
  >  n <- 1e5
  >  rho <- 0.99
  > 
  >  x <- arima.sim(model = list(ar = rho), n = n)
  >  gamma <- acf(x, lag.max = 1999, type = "covariance",
  +      plot = FALSE)$acf
  >  k <- seq(along = gamma)
  >  Gamma <- gamma[k %% 2 == 1] + gamma[k %% 2 == 0]
  >  k <- min(seq(along = Gamma)[Gamma < 0])
  >  Gamma <- Gamma[1:k]
  >  Gamma[k] < 0
  [1] TRUE
  >  Gamma[k] <- 0
  > 
  >  out <- .Call(mcmc:::C_initseq, x - mean(x))
  >  names(out)
  [1] "gamma0"    "Gamma.pos" "Gamma.dec" "Gamma.con" "var.pos"   "var.dec"  
  [7] "var.con"  
  > 
  >  all.equal(gamma[1], out$gamma0)
  [1] TRUE
  > 
  >  length(out$Gamma.pos) == length(Gamma)
  [1] TRUE
  >  all.equal(out$Gamma.pos, Gamma)
  [1] TRUE
  > 
  >  Gamma.dec <- cummin(Gamma)
  >  all.equal(out$Gamma.dec, Gamma.dec)
  [1] TRUE
  >  
  > ## IGNORE_RDIFF_BEGIN
  > library(Iso)
  Error in library(Iso) : there is no package called 'Iso'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'bfst.Rnw' using Sweave
--- finished re-building 'bfst.Rnw'

--- re-building 'debug.Rnw' using Sweave
--- finished re-building 'debug.Rnw'

--- re-building 'demo.Rnw' using Sweave

Error: processing vignette 'demo.Rnw' failed with diagnostics:
 chunk 19 (label = tab1) 
Error in library(xtable) : there is no package called 'xtable'

--- failed re-building 'demo.Rnw'

--- re-building 'morph.Rnw' using Sweave
Error in lud.induced(1:4) : 
  log unnormalized density function returned vector not scalar
--- finished re-building 'morph.Rnw'

SUMMARY: processing the following file failed:
  'demo.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'abind', 'chk', 'coda', 'extras', 'generics', 'lifecycle', 'nlist',
  'purrr', 'term', 'universals'

Packages suggested but not available for checking:
  'covr', 'readr', 'rlang', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'GIGrvg', 'loo', 'matrixStats', 'RcppEigen'

Packages suggested but not available for checking:
  'BayesLogit', 'lintools', 'spdep', 'maptools', 'bayesplot', 'coda',
  'posterior', 'testthat', 'roxygen2', 'knitr', 'rmarkdown', 'survey'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ellipse', 'Rcpp', 'fftwtools', 'testthat', 'RcppArmadillo'

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/mcmcse_vignette.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'sn', 'coda'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'rstan', 'overlapping', 'colorspace'

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:
  'survey', 'gee', 'dplyr', 'lme4', 'stringr', 'parameters'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BBmisc', 'ecr', 'checkmate', 'parallelMap', 'reshape2', 'gtools',
  'vegan', 'ggplot2', 'lhs'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'gridExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gbutils', 'Rdpack'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
do.linear.conjoint: no visible global function definition for
  'as.formula'
do.linear.conjoint: no visible global function definition for 'lm'
do.linear.conjoint: no visible global function definition for
  'coefficients'
is.close.to.orthogonal: no visible global function definition for 'cor'
mc.add.to.design: no visible global function definition for 'combn'
mc.good.designs: no visible global function definition for 'combn'
Undefined global functions or variables:
  as.formula coefficients combn cor lm
Consider adding
  importFrom("stats", "as.formula", "coefficients", "cor", "lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'scatterplot3d', 'testthat'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: 'bbmle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'multcomp', 'magic', 'MCMCpack', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R.utils', 'checkmate', 'R6'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DoseFinding'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'shiny', 'shinydashboard', 'devEMF', 'officer',
  'flextable', 'Rcpp', 'RcppNumerical', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'DoseFinding'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'future', 'future.apply', 'rjags', 'coda', 'loo', 'bayesplot',
  'tidybayes', 'dplyr', 'magrittr', 'tidyr', 'tidyselect', 'tibble',
  'stringr', 'ggplot2', 'patchwork', 'rlang'

Packages suggested but not available for checking:
  'hexbin', 'testthat', 'purrr', 'knitr', 'rmarkdown', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'quadprog', 'mvtnorm'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'multcomp'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'SMR', 'writexl', 'xtable', 'foreach', 'doParallel'

Package suggested but not available for checking: 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'RUnit', 'XML'
Package required but not available: 'CircStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'gridExtra', 'magrittr', 'rlang',
  'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Checking should be performed on sources prepared by 'R CMD build'.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'checkmate', 'cli', 'dplyr', 'hms', 'lifecycle', 'lubridate'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'knitr', 'mockr', 'readr', 'rmarkdown',
  'spelling', 'testthat', 'usethis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'testthat', 'rlang', 'Rdpack', 'simctest'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'igraph', 'ggplot2', 'purrr', 'magrittr', 'reshape2',
  'shiny', 'dplyr', 'psych', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'logistf', 'Rcpp', 'pcalg', 'mgm', 'bnlearn', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'devtools', 'roxygen2', 'knitr', 'testthat',
  'rmarkdown', 'spelling', 'httr', 'covr', 'gh', 'rlang', 'openssl',
  'git2r', 'pkgbuild', 'curl', 'VIM', 'FactoMineR', 'mice'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'earth', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: 'testthat'
Packages required but not available:
  'Rdpack', 'orthopolynom', 'foreach', 'doParallel', 'ggplot2', 'psych'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'ape', 'dendextend', '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: 'dplyr', 'tidyr'

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 suggested but not available for checking:
  'testthat', 'tibble', 'spelling'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'testthat', 'BH', 'psqn'

Packages suggested but not available for checking: 'testthat', 'catdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'RGtk2', 'coin'
'LazyData' is specified without a 'data' directory
Running examples in 'mdir.logrank-Ex.R' failed
The error most likely occurred in:

> ### Name: mdir.logrank
> ### Title: Two-sample multiple-direction log rank test
> ### Aliases: mdir.logrank
> 
> ### ** Examples
> 
> library(coin)
Error in library(coin) : there is no package called 'coin'
Execution halted
Package required but not available: 'futile.logger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RMySQL', 'shinydashboard', 'DBI', 'DT', 'leaflet', 'leaflet.extras',
  'shinyjs', 'ggplot2', 'dplyr', 'readxl', 'plotly', 'reactable',
  'writexl', 'xfun', 'berryFunctions', 'shinyWidgets', 'shiny',
  'htmltools', 'bslib', 'htmlwidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CDM', 'coda', 'miceadds', 'Rcpp', 'sirt', 'RcppArmadillo'

Packages which this enhances but not available for checking:
  'JointAI', 'jomo', 'mice', 'smcfcs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CompQuadForm', 'lme4', 'car'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reshape2', 'ggplot2', 'nloptr', 'rootSolve', 'psych', 'magic',
  'glmnet'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RColorBrewer', 'gplots', 'gtools'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'linprog'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Sleuth3'
Running examples in 'mdscore-Ex.R' failed
The error most likely occurred in:

> ### Name: summary.mdscore
> ### Title: Summary methods for mdscore objects
> ### Aliases: summary.mdscore
> ### Keywords: mdscore score glm
> 
> ### ** Examples
> 
> library(Sleuth3)
Error in library(Sleuth3) : there is no package called 'Sleuth3'
Execution halted
Packages required but not available: 'ellipse', 'mnormt', 'polycor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RColorBrewer', 'scatterplot3d', 'tcltk2', 'tkrplot', 'rpanel', 'rgl'

Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'smacof', 'princurve', 'rgl', 'reshape'

Packages suggested but not available for checking: 'qtl', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'smacof', 'clusterSim', 'symbolicDA', 'smds', 'animation', 'plotrix',
  'spdep'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'rmarkdown', 'dplyr', 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'parsedate', 'lubridate'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'babynames', 'DBI', 'dbplyr', 'downloader', 'dplyr', 'fs', 'ggplot2',
  'htmlwidgets', 'kableExtra', 'RMySQL', 'skimr', 'stringr', 'tibble',
  'webshot'

Packages suggested but not available for checking:
  'knitr', 'Lahman', 'leaflet', 'etl', 'macleish', 'mosaic',
  'mosaicData', 'lubridate', 'sf', 'testthat', 'utf8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'hrbrthemes', 'ggplot2', 'ggtext', 'ggthemes', 'tvthemes'

Package suggested but not available for checking: 'glue'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kyotil'

Packages suggested but not available for checking:
  'R.rsp', 'RUnit', 'Rmosek', 'mvtnorm', 'MethylCapSig', 'gtools'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'cli', 'httr', 'jsonlite', 'rappdirs'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'pastecs', 'png', 'tiff', 'dplR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dynlm', 'tdigest', 'hdrcde'

Packages suggested but not available for checking:
  'car', 'ConvergenceConcepts', 'geepack', 'lmtest', 'strucchange',
  'plm', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'ellipse', 'latentnet', 'vegan', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'lmerTest', 'numDeriv'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'BB', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringi', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', '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:
  'ggplot2', 'meteoland', 'Rcpp', 'shiny'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'multcomp', 'car', 'sandwich'

Packages suggested but not available for checking:
  'arm', 'gam', 'glmnet', 'mice', 'mitools', 'SuperLearner', 'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'rvest', 'xml2'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppNumerical', 'officer', 'flextable', 'devEMF', 'mvtnorm',
  'shiny', 'shinydashboard', 'shinyMatrix', 'foreach', 'doParallel',
  'doRNG', '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:
  'doParallel', 'doRNG', 'foreach', 'mvtnorm'

Packages suggested but not available for checking:
  'flextable', 'knitr', 'officer', 'rmarkdown', 'pander'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvest', 'xml2', 'lubridate', 'stopwords'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'sandwich', 'lpSolve', 'Hmisc', 'lme4'

Packages suggested but not available for checking:
  'quantreg', 'VGAM', 'SuppDists', 'testthat', 'speedglm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mediation', 'distr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'learnr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'plyr', 'reshape2', 'hash'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ggplot2', 'gridExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'ggplot2', 'maps', 'magrittr',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'audio', 'checkmate', 'deldir', 'wesanderson'

Package suggested but not available for checking: 'svglite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'rgdal', 'sp', 'raster', 'rgeos', 'hms', 'tibble', 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'patchwork', 'tm', 'wordcloud2'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jmvcore', 'R6', 'lavaan', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'curl', 'jsonlite', 'httr', 'stringr', 'rlang', 'vroom',
  'bib2df', 'tibble', 'progress', 'lubridate', 'purrr', 'data.table'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'kableExtra', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'matrixStats', 'seriation', 'stringdist', 'TraMineR',
  'WeightedCluster'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'viridisLite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'survey', 'lavaan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'mvtnorm', 'matrixcalc'

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', 'purrr', 'dplyr', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mefa'
Package unavailable to check Rd xrefs: 'mefa'
Running 'mefa4comparisons.R'
Running the tests in 'tests/mefa4comparisons.R' failed.
Complete output:
  > ## performance comparison
  > library(mefa)
  Error in library(mefa) : there is no package called 'mefa'
  Execution halted
Packages suggested but not available for checking: 'vegan', 'mefa4'
Package unavailable to check Rd xrefs: 'vegan'
Packages required but not available:
  'SKAT', 'pedgene', 'gdsfmt', 'AnnotationDbi', 'DBI', 'GenomeInfoDb',
  'RSQLite', 'famSKATRC', 'kinship2', 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'formatR', 'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'org.Hs.eg.db'

VignetteBuilder 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', 'igraph', 'Rcpp', 'ggplot2', 'reshape',
  'fpc', 'ggrepel', 'ggraph', 'BH'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'leaps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppEigen', 'RcppProgress'

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', 'R6', 'rlang', 'tibble', 'cpp11'

Packages suggested but not available for checking:
  'clipr', 'covr', 'crayon', 'curl', 'readr', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'plyr', 'dplyr', 'reticulate', 'Rcpp', 'shiny', 'shinyjs',
  'tidyr', 'leaflet', 'tibble', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'shinydashboard', 'shinyWidgets', 'shinyBS',
  'shinyjs', 'RColorBrewer', 'tidyr', 'dplyr', 'openxlsx', 'haven',
  'readxl', 'stringr', 'stringi', 'DT', 'RODBC', 'formattable',
  'ggplot2', 'plotly', 'mem'

Packages suggested but not available for checking: 'magick', 'animation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gridGraphics', 'magick', 'showtext', 'sysfonts'

Packages suggested but not available for checking:
  'cowplot', 'ggimage', 'knitr', 'rmarkdown', 'prettydoc', 'shadowtext'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'showtext', 'sysfonts', 'png', 'jpeg', 'Cairo', 'ggplot2', 'cowplot',
  'magrittr', 'purrr', 'shiny', 'shinycssloaders', 'shinyBS',
  'colourpicker'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'magick', 'gifski'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'gdistance', 'raster', 'sp', 'vegan'

Packages suggested but not available for checking:
  'adegenet', 'geosphere', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/memgeneTutorial.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'repr', 'data.table'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'sandwich'

Packages which this enhances but not available for checking:
  'AER', 'car', 'eha', 'lme4', 'ordinal', 'simex', 'tibble', 'haven'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'urca', 'forecast', 'fracdiff', 'LongMemoryTS', 'sandwich',
  'strucchange', 'longmemo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'xts', 'zoo', 'data.table'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'digest', 'uuid', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bookdown', 'rmarkdown', 'usethis'

Packages suggested but not available for checking:
  'knitr', 'pkgdown', 'rmdformats', 'testthat'

VignetteBuilder 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', 'cachem'

Packages suggested but not available for checking:
  'digest', 'aws.s3', 'covr', 'googleAuthR', 'googleCloudStorageR',
  'httr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'digest'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ranger', 'cowplot', 'viridis', 'viridisLite', 'zoo',
  'stringr', 'HH', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'formatR', 'kableExtra', 'magrittr', 'knitr',
  'rmarkdown', 'rpart.plot', 'randomForest', 'virtualPollen'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'yaml', 'rmarkdown', 'knitr'

Packages suggested but not available for checking: 'kableExtra', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sm', 'RColorBrewer', 'mclust', 'ggplot2', 'tidyr', 'dplyr', 'purrr',
  'RcppRoll', 'EnvStats'

Package suggested but not available for checking: 'magick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'rmarkdown', 'plotly', 'ggplot2', 'robustbase', 'iterpc',
  'quantreg', 'rjson', 'glmnet'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'mvtnorm', 'pracma', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Thresher', 'Rtsne', 'ClassDiscovery', 'Polychrome', 'dendextend',
  'igraph', 'flexmix', 'umap', 'kohonen'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'nonnest2', 'sandwich', 'lavaan', 'numDeriv'

Packages suggested but not available for checking:
  'tinytest', 'mirt', 'lmeInfo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'randomizeR'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randtoolbox', 'statmod'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'missForest', 'ggpubr', 'progress', 'doParallel', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'arm', 'lme4', 'dplyr', 'mvtnorm', 'foreach', 'shiny', 'abind',
  'ggplot2', 'blme', 'broom.mixed'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'future.apply', 'rstanarm',
  'Amelia', 'DT'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'glue', 'rlang', 'magrittr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'abind', 'rmarkdown', 'knitr', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'glue', 'magrittr', 'rlang', 'stringr'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'geepack', 'geeM', 'ggplot2', 'ggformula', 'glmnet',
  'kinship2', 'mvtnorm', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'lme4', 'magrittr', 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'purrr', 'lubridate', 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'covr', '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: 'sp', 'shiny', 'shinyBS', 'caTools'

Package suggested but not available for checking: 'INLA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'ggvis', 'DT', 'rstudioapi'

Package suggested but not available for checking: 'rmeta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'GenABEL'
Malformed Description field: should contain one or more complete sentences.
dometa: no visible global function definition for 'qchisq'
dometa: no visible global function definition for 'median'
dometa: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'qnorm'
forestplot: no visible global function definition for 'points'
forestplot: no visible global function definition for 'text'
metagwa.files: no visible global function definition for 'read.csv'
metagwa.files: no visible global function definition for 'write.csv'
metagwa.tables: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  median pchisq points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'bridgesampling', 'coda', 'LaplacesDemon', 'logspline',
  'mvtnorm', 'RcppParallel', 'rstan', 'rstantools', 'BH', 'RcppEigen',
  'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'fs', 'magrittr', 'piggyback', 'purrr', 'readr', 'rlang',
  'stringr', 'tibble', 'yaml'

Packages suggested but not available for checking:
  'testthat', 'covr', '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:
  'mclust', 'mvtnorm', 'ellipse', 'gtools', 'gplots'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'magrittr', 'usethis', 'dplyr', 'ggplot2', 'ggfittext',
  'cli', 'forcats', 'ggimage', 'patchwork', 'scales', 'stringr',
  'tidyr', 'purrr', 'meta', 'glue', 'rmarkdown'

Packages suggested but not available for checking:
  'knitr', 'here', 'Rd2roxygen', 'kableExtra', 'fansi', 'downloadthis',
  'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'superpc', 'glmnet', 'matrixStats', 'survminer', 'rms', 'tidyr',
  'pls', 'Rdpack', 'ggplot2', 'dplyr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'httr', 'dplyr', 'purrr', 'crayon'

Packages suggested but not available for checking:
  'covr', 'testthat', 'tibble', 'knitr', 'rmarkdown', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'enviPick', 'ggplot2', 'scales', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'C50', 'caret', 'e1071', 'mixOmics', 'pcaMethods', 'plyr', 'ropls',
  'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gridExtra', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MLmetrics', 'xcms', 'reshape2', 'knitr', 'ggplot2', 'plotrix',
  'klaR', 'fastAdaboost', 'randomForest', 'kernlab', 'BiocStyle',
  'graph', 'Rgraphviz', 'caret'

Package suggested but not available for checking: 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'factoextra', 'dbscan', 'dplyr', 'seqinr', 'Biostrings'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'ggplot2', 'igraph', 'taxize', 'seqinr', 'RCurl', 'ape',
  'lazyeval', 'dplyr', 'magrittr', 'readr', 'rlang', 'ggfittext',
  'vegan', 'cowplot', 'GA', 'Rcpp', 'crayon', 'tibble', 'R6'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'zlibbioc', 'BiocManager',
  'phyloseq', 'phylotate', 'traits', 'biomformat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reshape2', 'plyr', 'dplyr', 'data.table', 'ggplot2', 'Cairo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vegan'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ellipsis', 'forcats', 'ggplot2', 'glue', 'magrittr',
  'purrr', 'rlang', 'shiny', 'stringr', 'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'covr', 'knitr', 'metafor', 'patchwork', 'readr', 'rio', 'rmarkdown',
  'roxygen2', '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:
  'R6', 'tidyr', 'dplyr', 'stringr', 'magrittr', 'XML', 'purrr',
  'readxl', 'rlang', 'tibble', 'tidyselect'

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: 'rmeta', 'gsl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'ggplot2', 'httr', 'jsonlite', 'progress',
  'tidyr', 'verification'

Packages suggested but not available 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: 'gnm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mathjaxr'

Packages suggested but not available for checking:
  'metafor', 'numDeriv', 'BiasedUrn', 'dfoptim', 'igraph', 'ape',
  'testthat', 'digest', 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvest', 'RCurl', 'XML', 'SPARQL', 'pacman', 'rcdk', 'rJava',
  'pbapply', 'enviPat', 'data.table', 'RSQLite', 'DBI', 'gsubfn',
  'stringr', 'WikidataQueryServiceR', 'webchem', 'jsonlite', 'R.utils',
  'KEGGREST', 'zip', 'ChemmineR', 'xml2', 'stringi', 'reshape2',
  'Hmisc', 'httr', 'RJSONIO', 'readxl', 'cmmr', 'progress', 'Rdisop',
  'rlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magick', 'purrr'

Packages suggested but not available for checking:
  'mockery', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'metadynminer', 'rgl', 'Rcpp', 'misc3d'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gridExtra', 'caret', 'ggplot2', 'e1071', 'gbm', 'randomForest'

Packages suggested but not available for checking: 'knitr', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'plyr', 'colorspace', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'devtools', 'TeachingDemos', 'RColorBrewer', 'reshape2'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/metafolio.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'metafor', 'ranger', 'data.table', 'gtable'

Packages suggested but not available for checking:
  'testthat', 'caret', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mathjaxr', 'pbapply'

Packages suggested but not available for checking:
  'lme4', 'numDeriv', 'minqa', 'nloptr', 'dfoptim', 'ucminf',
  'optimParallel', 'CompQuadForm', 'mvtnorm', 'BiasedUrn', 'Epi',
  'GLMMadaptive', 'multcomp', 'gsl', 'sp', 'ape', 'crayon', 'R.rsp',
  'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'evd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'metafor', 'rlang'

Packages suggested but not available for checking:
  'roxygen2', 'knitr', 'rmarkdown', 'devtools', 'covr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'metafor', 'stringr'

Packages suggested but not available for checking:
  'EBImage', 'ape', 'hexView', 'RCurl', 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rsolnp', 'corpcor', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BiocManager', 'rmeta', 'multtest', 'ggplot2', 'Rmisc', 'gplots',
  'Biobase', 'RMySQL', 'DBI', 'stringr', 'preprocessCore', 'GEOquery',
  'GEOmetadb', 'RSQLite', 'data.table', 'ggpubr', 'ROCR', 'zoo',
  'pracma', 'COCONUT', 'Metrics', 'manhattanly', 'DT', 'pheatmap',
  'plyr', 'dplyr', 'reshape2', 'rmarkdown', 'AnnotationDbi',
  'HGNChelper', 'magrittr', 'readr', 'plotly', 'httpuv'

Packages suggested but not available for checking:
  'BiocStyle', 'knitr', 'RUnit', 'BiocGenerics', 'snplist', 'magick'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dataone', 'dplyr', 'EML', 'emld', 'lubridate', 'purrr', 'readr',
  'stringr', 'tibble', 'tidyr', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'udunits2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'e1071', 'fgui', 'googleVis', 'maptools', 'rgeos',
  'rgrass7', 'raster', 'spatstat.geom', 'spatstat.random', 'sp',
  'minpack.lm', 'zipfR', 'coda', 'knitr'

Package suggested but not available for checking: 'rasterVis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gss', 'plyr', 'zoo', 'pracma', 'ggplot2', 'doParallel',
  'metagenomeSeq', 'DESeq2', 'edgeR'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'openxlsx', 'dplyr', 'tidyr', 'tibble', 'agricolae', 'rlang'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'limma', 'SMVar'

Packages suggested but not available for checking:
  'GEOquery', 'org.Hs.eg.db', 'VennDiagram', 'annaffy',
  'hgu133plus2.db', 'hgu133a.db', 'hgu95av2.db'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'estmeansd', 'Hmisc', 'metafor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'FNN', 'progress'

Packages suggested but not available for checking:
  'shiny', 'miniUI', 'testthat', 'data.table', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gamlss', 'meta', 'lme4', 'gdata', 'plyr', 'dplyr', 'tidyr',
  'ggplot2', 'gridExtra', 'lmerTest', 'matrixStats', 'zCompositions',
  'compositions'

Packages suggested but not available for checking:
  'testthat', 'RCurl', 'httr', 'repmis', 'jsonlite', 'knitr',
  'rmarkdown', 'gplots', 'magrittr', 'reshape2', 'caret',
  'randomForest', 'tsibble', 'RColorBrewer'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'metafor', 'mvtnorm', 'lme4', 'dplyr', 'plyr', 'pROC', 'ggplot2'

Packages suggested but not available for checking:
  'coda', 'runjags', 'rjags', 'ggmcmc', 'logistf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'gtools', 'Rmpi', 'ggplot2'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/guide.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'GGally', 'ggforce', 'ggplot2', 'ggrepel', 'lme4',
  'lmerTest', 'magrittr', 'mathjaxr', 'patchwork', 'purrr', 'rlang',
  'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'DT', 'knitr', 'rmarkdown', 'roxygen2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'gridExtra', 'Formula', 'RcppArmadillo',
  'RcppProgress', 'BH'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Biobase', 'GSEABase', 'genefilter', 'impute'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'encode', 'magrittr', 'dplyr', 'tidyr', 'rlang', 'gridExtra',
  'gtable', 'ggplot2', 'scales'

Package suggested but not available for checking: 'csv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gridExtra'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'metafor'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bbmle', 'metafor', 'numDeriv', 'fastGHQuad', 'lme4', 'Rfast',
  'doParallel', 'foreach', 'doRNG'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gridBezier'

Package suggested but not available for checking: 'grImport'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'knitr', 'magrittr', 'tidyr',
  'testthat', 'rlang'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'TFisher', 'mutoss', 'mathjaxr', 'qqconf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'dendextend', 'dplyr', 'ggforce', 'ggrepel', 'reshape2',
  'stringr', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'metafor', 'lme4', 'CompQuadForm', 'xml2'

Package suggested but not available for checking: 'BiasedUrn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'meta'

Packages suggested but not available for checking:
  'metafor', 'lme4', 'numDeriv', 'BiasedUrn', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstpm2', 'mvmeta', 'meta', 'survRM2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'DESeq2', 'VennDiagram'
Error(s) in re-building vignettes:
--- re-building 'metaRNASeq.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "metaRNASeq.tex" --max-iterations=20 -I "C:/r_packages/rinst/share/texmf/tex/latex" -I "C:/r_packages/rinst/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
running 'texi2dvi' on 'metaRNASeq.tex' failed

LaTeX errors:
ignettes/metaRNASeq.tex:432: Package pdftex.def Error: File `venn_jpeg.jpg' not
 found: using draft setting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.

--- failed re-building 'metaRNASeq.Rnw'

SUMMARY: processing the following file failed:
  'metaRNASeq.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ordinal', 'maxLik', 'truncnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'OpenMx', 'ellipse', 'mvtnorm', 'numDeriv', 'lavaan'

Packages suggested but not available for checking:
  'metafor', 'semPlot', 'R.rsp', 'testthat'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'meta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'loo', 'forestplot', 'metafor',
  'HDInterval', 'coda', 'StanHeaders', 'BH', 'RcppEigen',
  'RcppParallel'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'shinystan', 'vdiffr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'knitr', 'magrittr', 'purrr'

Packages suggested but not available for checking:
  'rmarkdown', 'shiny', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'mpt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'meta', 'powerSurvEpi', 'readxl', 'withr', 'writexl', 'xtable'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat', 'spelling', 'DT', 'epiR', 'esc',
  'pwr', 'metafor'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'metafor', 'metadat', 'stringr', 'purrr', 'dplyr', 'tidyr', 'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'mvmeta', 'metaSEM', 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'nullabor', 'dplyr', 'RColorBrewer', 'metafor',
  'gridExtra', 'ggpubr'

Packages suggested but not available for checking:
  'Cairo', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'metafor', 'dplyr', 'forestmodel', 'magrittr', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'roxygen2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'raster', 'sp', 'zoo', 'ncdf4', 'XML'

Packages suggested but not available for checking: 'rgdal', 'rasterVis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'RadioSonde'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'sf', 'spdep', 'rgdal', 'ncdf4', 'meteospain', 'Rcpp', 'units'

Packages suggested but not available for checking:
  'knitr', 'forecast', 'spacetime', 'stars', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sp', 'spacetime', 'rgdal', 'gstat', 'raster', 'snowfall', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pracma', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'crayon', 'dplyr', 'glue', 'httr', 'jsonlite',
  'lubridate', 'magrittr', 'purrr', 'rlang', 'sf', 'stringr', 'tidyr',
  'units', 'xml2', 'vctrs', 'memoise', 'cachem'

Packages suggested but not available for checking:
  'ggforce', 'ggplot2', 'keyring', '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: 'nleqslv', 'distr'

Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'astroFns', 'lubridate', 'plotrix', 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'chron', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coda', 'rjags'

Package suggested but not available for checking: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'dplyr', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'reshape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
RUVRand: no visible global function definition for 'barplot'
RUVRand: no visible global function definition for 'prcomp'
RuvRandIter: no visible global function definition for 'kmeans'
RuvRandIter: no visible global function definition for 'barplot'
RuvRandIter: no visible global function definition for 'prcomp'
opt: no visible global function definition for 'optim'
printdata: no visible global function definition for 'head'
Undefined global functions or variables:
  barplot head kmeans optim prcomp
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "kmeans", "optim", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'scales', 'stringr', 'tibble', 'lubridate', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lubridate'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gplots', 'fastcluster'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'htmlwidgets', 'htmltools'

Packages suggested but not available for checking:
  'testthat', 'RColorBrewer', 'ggplot2', 'ggplot2movies', 'jsonlite',
  'knitr', 'shiny', 'binom', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'dplyr', 'rmarkdown', '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: 'numDeriv', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'coda'

Packages suggested but not available for checking: 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geodist', 'hms', 'httr', 'jsonlite', 'tibble'

Packages suggested but not available for checking:
  'covr', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'digest', 'fields', 'Formula',
  'formula.tools', 'ggplot2', 'gtable', 'memoise', 'plyr', 'scales',
  'sp', 'stringr', 'purrr', 'RCurl', 'isoband', 'lubridate'

Packages suggested but not available for checking:
  'maps', 'maptools', 'covr', 'irlba', 'knitr', 'ncdf4', 'pkgdown',
  'reshape2', 'rmarkdown', 'testthat', 'viridis', 'udunits2', 'PCICt',
  'gridExtra', 'vdiffr', 'proj4', 'kriging', 'raster', 'rgdal', 'here'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geosphere', 'matlab', 'leaflet', 'plyr', 'RCurl'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'MetabolAnalyze', 'Rfast', 'shiny',
  'shinythemes', 'vroom'

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:
  'timereg', 'lava', 'mvtnorm', 'numDeriv', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'optimx', 'prodlim', 'cmprsk', 'testthat', 'ucminf', 'knitr',
  'rmarkdown', 'ggplot2', 'cowplot', 'icenReg'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'readr', 'stringr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'alabama', 'evd', 'nleqslv', 'nloptr', 'Rcpp', 'TruncatedNormal',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'cobs', 'knitr', 'mvPot', 'mvtnorm', 'gmm', 'revdbayes', 'ismev'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/mev-vignette.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
show,mewTyp: no visible global function definition for 'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
Packages required but not available: 'statmod', 'numDeriv', 'lamW'

Package suggested but not available for checking: 'rstpm2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qusage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'matrixcalc', 'face'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'lubridate', 'GIGrvg', 'stochvol', 'RcppParallel',
  'dplyr', 'magrittr', 'tibble', 'zoo', 'RcppArmadillo', 'RcppProgress'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'ggridges', 'alfred', 'factorstochvol'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/mfbvar_jss.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'logging', 'DBI', 'duckdb', 'getPass', 'rlang', 'RPostgres',
  'RSQLite'

Packages suggested but not available for checking:
  'dplyr', 'dbplyr', 'knitr', 'rmarkdown', 'unittest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numbers'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'ape', 'betapart', 'dendextend', 'FactoMineR', 'gawdis',
  'geometry', 'ggplot2', 'ggrepel', 'Hmisc', 'patchwork', 'reshape2',
  'rstatix', 'vegan'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'magrittr', 'rmarkdown', 'stringr', 'tibble',
  'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clusterCrit', 'ECoL', 'e1071', 'infotheo', 'rrcov'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'numDeriv', 'zoo', 'maxLik'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'covr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fda.usc', 'deldir', 'depth', 'depthTools', 'matrixStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tseries', 'pastecs', 'locfit', 'tseriesChaos', 'tsDyn', 'forecast'
Packages required but not available: 'dtw', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', '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', 'ggplot2', 'magrittr', 'tibble', 'minpack.lm', 'openxlsx',
  'readxl', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'funData', 'abind', 'foreach', 'irlba', 'plyr'

Packages suggested but not available for checking:
  'covr', 'fda', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available:
  'Ball', 'reticulate', 'crayon', 'cli', 'dr', 'foreach', 'doParallel',
  'fs'

Packages suggested but not available for checking:
  'knitr', 'randomForestSRC', 'SIS', 'glmnet', 'ncvreg', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ars', 'HI', 'coda'

Packages suggested but not available for checking:
  'sns', 'RcppArmadillo', 'inline', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sandwich', 'lmtest', 'betareg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tseries', 'mvtnorm'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dataRetrieval', 'lmomco'
Packages required but not available: 'abind', 'energy', 'raster'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'reshape2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'qgam', 'ggplot2', 'gamm4', 'matrixStats', 'viridis', 'GGally',
  'gridExtra', 'plyr', 'shiny', 'miniUI'

Packages suggested but not available for checking:
  'rgl', 'knitr', 'rmarkdown', 'testthat', 'webshot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'deSolve'

Packages suggested but not available for checking:
  'MGDrivE', 'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'Rcpp', 'Rdpack'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

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:
  'corpcor', 'gridExtra', 'R.utils', 'reticulate'

Packages suggested but not available for checking:
  'knitr', 'mvtnorm', '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: 'mvabund', 'snowfall'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggplot2', 'plyr', 'reshape2', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'mvnfast', 'plyr', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  '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:
  'glmnet', 'stringr', 'Hmisc', 'qgraph', 'gtools'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MALDIquant', 'MALDIquantForeign'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'evd', 'numDeriv', 'corpcor', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'RJSONIO'
'library' or 'require' call to 'RJSONIO' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for 'packageVersion'
.onAttach: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible global function definition for 'fromJSON'
call.MGRAST: no visible binding for global variable '.MGRAST'
call.MGRAST: no visible global function definition for 'download.file'
call.MGRAST: no visible global function definition for 'isValidJSON'
call.MGRAST: no visible global function definition for 'fromJSON'
doc.MGRAST: no visible binding for global variable '.MGRAST'
doc.MGRAST: no visible global function definition for 'str'
load.MGRAST: no visible binding for global variable '.MGRAST'
parse.MGRAST: no visible binding for global variable '.MGRAST'
this.package: no visible binding for global variable '.MGRAST'
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'combinat', 'statmod'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown'

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: 'Biobase', 'GSA', 'limma', 'ismev'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'sp', 'leaflet', 'spgwr', 'doParallel', 'foreach',
  'htmltools', 'nabor', 'RcppEigen'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
BCI: no visible global function definition for 'quantile'
Metro_Hastings: no visible global function definition for 'optim'
Metro_Hastings: no visible global function definition for 'runif'
Metro_Hastings: no visible global function definition for 'var'
plotMH: no visible global function definition for 'hist'
plotMH: no visible global function definition for 'frame'
plotMH: no visible global function definition for 'text'
Undefined global functions or variables:
  frame hist optim quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'plot3D', 'rootSolve', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rappdirs', 'reticulate', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'MCMCpack', 'mvtnorm', 'Rdpack'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'alluvial', 'RColorBrewer', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'reshape2', 'gridExtra', 'RcppArmadillo', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/vignette1.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'structSSI', 'MHTdiscrete', 'FixSeqMTP'
Package unavailable to check Rd xrefs: 'MHTdiscrete'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Formula', 'truncreg', 'maxLik', 'Rdpack', 'prediction', 'margins',
  'generics', 'numDeriv'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'lmtest', 'xtable', 'bookdown', 'texreg',
  'testthat'

VignetteBuilder 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', 'foreach', 'imp4p', 'impute', 'limma', 'mice', 'stringr'

Packages suggested but not available for checking:
  'Biobase', 'knitr', 'R.rsp', 'markdown', 'prettydoc', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'e1071', 'raster', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mice', 'mitools', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'BIFIEsurvey', 'blme', 'car', 'CDM', 'coda', 'grouped', 'imputeR',
  'inline', 'lme4', 'MBESS', 'MCMCglmm', 'mdmb', 'numDeriv', 'readxl',
  'sandwich', 'simputation', 'sirt', 'sjlabelled', 'synthpop', 'TAM'

Packages which this enhances but not available for checking:
  'Amelia', 'jomo', 'micemd', 'mitml', 'pan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pROC', 'rms', 'mice', 'mitml', 'mitools', 'dplyr', 'purrr', 'tidyr',
  'tibble', 'stringr', 'car', 'rlang', 'magrittr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'bookdown', 'readr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lmtest', 'micEcon', 'systemfit', 'miscTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'minpack.lm', 'DEoptim', 'car', 'systemfit', 'micEcon', 'miscTools'

Packages suggested but not available for checking:
  'maxLik', 'xtable', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'miscTools'

Packages suggested but not available for checking: 'Ecdat', 'micEcon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'miscTools', 'plm'

Packages suggested but not available for checking: 'Ecdat', 'systemfit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'miscTools', 'systemfit'

Package suggested but not available for checking: 'micEcon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'data.table', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pacman', 'testthat', 'mice', 'magrittr',
  'ggplot2', 'UpSetR', '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:
  'mice', 'lme4', 'mvmeta', 'jomo', 'mvtnorm', 'digest', 'abind'

Package suggested but not available for checking: 'VIM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ranger', 'data.table', 'FNN', 'ggplot2', 'crayon', 'corrplot',
  'ggpubr', 'DescTools', 'foreach'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'doParallel', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'dplyr', 'generics', 'Rcpp', 'rlang', 'tidyr', 'withr',
  'cpp11'

Packages suggested but not available for checking:
  'broom.mixed', 'decor', 'glmnet', 'haven', 'knitr', 'lme4', 'lmtest',
  'metafor', 'mitml', 'miceadds', 'pan', 'randomForest', 'ranger',
  'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magrittr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doBy', 'combinat', 'flexclust', 'irr', 'matrixStats'

Packages suggested but not available for checking:
  'knitr', 'xtable', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'biotools', 'MVN', 'deseasonalize', 'testthat', 'knitr', 'roxygen2',
  'devtools'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/paper.Rnw'
   'inst/doc/tolatex-examples.Rnw'
(Is a VignetteBuilder field missing?)
Packages unavailable to check Rd xrefs: 'MVN', 'biotools'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/paper.Rnw'
   'vignettes/tolatex-examples.Rnw'
(Is a VignetteBuilder field missing?)
Running examples in 'micompr-Ex.R' failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright (c) 2016 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'nleqslv', 'distr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ggplot2', 'multcomp', 'RUnit'
Packages required but not available:
  'dplyr', 'plyr', 'magrittr', 'broom', 'phyloseq', 'vegan', 'rlang',
  'ggplot2', 'ggpubr', 'DESeq2', 'SummarizedExperiment', 'S4Vectors',
  'rstatix', 'tidyr', 'phangorn', 'randomForest', 'edgeR', 'testthat'

Packages suggested but not available for checking:
  'markdown', 'dada2', 'rmarkdown', 'knitr', 'Biostrings', 'DECIPHER'

VignetteBuilder 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', 'matrixStats', 'statmod', 'ggrepel', 'lmerTest',
  'foreach', 'modeest', 'phyloseq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'microseq', 'microcontax', 'dplyr', 'stringr', 'rlang', 'Rcpp',
  'RcppParallel', 'tibble', 'RcppEigen'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'microseq'

Package suggested but not available for checking: 'microcontax.data'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'jsonlite', 'data.table', 'tibble', 'httpcode'

Packages suggested but not available for checking: 'testthat', 'vcr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'ape', 'vegan', 'rlang', 'data.table', 'magrittr', 'dplyr',
  'tibble', 'scales', 'ggplot2', 'RColorBrewer', 'reshape2'

Packages suggested but not available for checking:
  'GUniFrac', 'ggpubr', 'randomForest', 'ggdendro', 'ggrepel',
  'agricolae', 'gridExtra', 'picante', 'pheatmap', 'igraph', 'rgexf',
  'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DT', 'dplyr', 'ggplot2', 'gtools', 'magrittr', 'scales', 'shiny',
  'shinyBS', 'tidyr', 'shinyWidgets', 'ggiraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'maptools', 'RColorBrewer', 'rgdal', 'sp', 'sf', 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rgeos'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RColorBrewer', 'stringr', 'labeling'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'extraDistr', 'abind', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'data.table', 'callr',
  'httr', 'readr', 'withr', 'plumber'

VignetteBuilder 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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'microseq', 'dplyr', 'stringr', 'igraph', 'tibble', 'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Hmisc', 'HH', 'flextable', 'officer', 'ggplot2', 'htmltools',
  'cowplot'

Packages suggested but not available for checking:
  'reshape2', 'latticeExtra', 'xtable', 'markdown', 'rmarkdown',
  'knitr', 'htmlTable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'deSolve', 'visNetwork', 'testthat'

Packages suggested but not available for checking:
  'rmarkdown', 'R.rsp', 'knitr', '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:
  'Rcpp', 'abind', 'deSolve', 'devtools', 'ggplot2', 'gridExtra',
  'gtools', 'knitr', 'matrixStats', 'matrixcalc', 'plyr', 'readr',
  'reshape2', 'shiny', 'stringr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'bookdown', 'data.table', 'plotly', 'shinyjs', 'shinyBS',
  'rmarkdown', 'rhandsontable', 'shinycssloaders', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyr', 'openxlsx', 'data.table', 'R.utils', 'stringr', 'magrittr',
  'dplyr', 'gtools', 'Biostrings', 'GenomicAlignments', 'Rsamtools',
  'GenomeInfoDb', 'BiocGenerics'

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'stringr', 'dplyr', 'data.table', 'rlang', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'config', 'desc', 'dplyr', 'glue', 'purrr', 'withr'

Packages suggested but not available for checking:
  'testthat', 'usethis', 'httptest', 'plumber', 'pkgload', 'jsonlite',
  'promises', 'future', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'ascii', 'BH'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AzureAuth', 'AzureGraph', 'curl', 'httr', 'jsonlite', 'R6', 'vctrs',
  'mime'

Packages suggested but not available for checking:
  'openssl', 'knitr', 'rmarkdown', 'testthat', 'blastula', 'emayili'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crayon', 'fmsb', 'future', 'future.apply', 'ggplot2', 'ggside',
  'progressr', 'reshape2', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'survey', 'kernlab', 'LowRankQP', 'nleqslv', 'pracma'

Packages suggested but not available for checking:
  'xlsx', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'chron', 'snowfall', 'rlecuyer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'gbm', 'genefilter', 'limma', 'preprocessCore', 'pROC',
  'SQN'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MCMCpack', 'coda', 'R2jags'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doRNG', 'doParallel', 'foreach', 'mcGlobaloptim', 'lubridate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sandwich', 'optimx', 'quantreg', 'numDeriv', 'forecast', 'zoo',
  'Formula', 'texreg'

Packages suggested but not available for checking:
  'testthat', 'lubridate', 'xts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mice'
'LazyData' is specified without a 'data' directory
Running examples in 'midastouch-Ex.R' failed
The error most likely occurred in:

> ### Name: mice.impute.midastouch
> ### Title: Predictive Mean Matching with distance aided selection of donors
> ### Aliases: mice.impute.midastouch midastouch
> ### Keywords: mice
> 
> ### ** Examples
> 
> ## from R:: mice, slightly adapted ##
> 
> # do default multiple imputation on a numeric matrix
> library(midastouch)
> library(mice)
Error in library(mice) : there is no package called 'mice'
Execution halted
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BiasedUrn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SMR', 'writexl', 'xtable'

Packages suggested but not available for checking:
  'tkrplot', 'testthat', 'knitr', 'rmarkdown', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mice', 'dplyr', 'checkmate'

Packages suggested but not available for checking:
  'psych', 'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'tidyr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'stringr', 'magrittr', 'tibble',
  'forcats', 'matrixStats', 'migration.indices', 'circlize'

Packages suggested but not available for checking:
  'spelling', 'tidyverse', 'countrycode'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggdendro', 'ggraph', 'ggplot2', 'gridExtra', 'igraph',
  'magrittr', 'network', 'oaqc', 'purrr', 'RColorBrewer', 'rlang',
  'sna', 'stringr', 'tibble', 'tidygraph', 'tidyr', 'concaveman',
  'ggforce', 'readxl'

Packages suggested but not available for checking:
  'covr', 'knitr', 'patchwork', '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:
  'dplyr', 'tidyr', 'tibble', 'rlang', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'calibrate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gWidgets2', 'mi', 'arm'

Package suggested but not available for checking: 'gWidgets2RGtk2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mstate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ppcor', 'Rcpp', 'scales'

Packages suggested but not available for checking:
  'igraph', 'ggplot2', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R2jags', 'matlib'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lavaan', 'numDeriv', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'dplyr', 'e1071', 'glmnet', 'kernlab', 'MLmetrics',
  'randomForest', 'rlang', 'xgboost'

Packages suggested but not available for checking:
  'doFuture', 'foreach', 'future', 'future.apply', 'ggplot2', 'knitr',
  'progress', 'progressr', 'purrr', 'rmarkdown', 'testthat', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
nat_hist: no visible global function definition for 'data'
nat_hist: no visible binding for global variable 'current.other'
t_mal: no visible global function definition for 'uniroot'
t_prog: no visible global function definition for 'rlnorm'
tdeath_lung: no visible global function definition for 'data'
tdeath_lung: no visible binding for global variable 'ci.lung'
tdeath_lung: no visible binding for global variable 'current.other'
tdeath_lung: no visible binding for global variable 'former.other'
tdeath_lung: no visible binding for global variable 'never.other'
tdeath_other: no visible global function definition for 'data'
tdeath_other: no visible binding for global variable 'ci.lung'
tdeath_other: no visible binding for global variable 'current.other'
tdeath_other: no visible binding for global variable 'former.other'
tdeath_other: no visible binding for global variable 'never.other'
Undefined global functions or variables:
  ci.lung current.other data former.other never.other rlnorm uniroot
Consider adding
  importFrom("stats", "rlnorm", "uniroot")
  importFrom("utils", "data")
to your NAMESPACE file.
Packages required but not available: 'data.table', 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gaston', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'png'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pipeR', 'numDeriv', 'glmnet', 'Rcpp', 'RcppParallel',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'Hmisc', 'rmarkdown', 'data.table', 'ggplot2',
  'plyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'softImpute', 'FactoMineR', 'doParallel', 'foreach',
  'data.table', 'rARPACK'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mitools'
Malformed Description field: should contain one or more complete sentences.
MImix.default: no visible binding for global variable 'coef'
MImix.default: no visible binding for global variable 'vcov'
MImix.one: no visible global function definition for 'qnorm'
MImix.one: no visible global function definition for 'uniroot'
mixcdf.target: no visible global function definition for 'pnorm'
print.MImixresult: no visible global function definition for 'coef'
print.MImixresult: no visible global function definition for 'vcov'
summary.MImixresult: no visible global function definition for 'coef'
summary.MImixresult: no visible global function definition for 'vcov'
summary.MImixresult: no visible global function definition for 'qt'
Undefined global functions or variables:
  coef pnorm qnorm qt uniroot vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "qt", "uniroot", "vcov")
to your NAMESPACE file.
Running examples in 'MImix-Ex.R' failed
The error most likely occurred in:

> ### Name: diaph.data
> ### Title: Diaphanography Partial Verification Bias Example
> ### Aliases: diaph.data
> 
> ### ** Examples
> 
> data(diaph.data)
> attach(diaph.data)
> ## Calculate sensitivity for each imputed table
> 
> sens.imps<-lapply(imputed.tables,function(x){ x[2,2]/(x[2,1]+x[2,2]) })
> sens.imps.vars<-lapply(imputed.tables,function(x){ x[2,2]*x[2,1]/(x[2,1]+x[2,2])^3 })
> 
> ### Calculate mixture summary
> 
> MImix(sens.imps,sens.imps.vars)
  2.5%ile    50%ile  97.5%ile 
0.1667023 0.2989993 0.5167686 
> 
> ### Compare to usual t-summary using MIcombine: requires(mitools)
> 
> library(mitools)
Error in library(mitools) : there is no package called 'mitools'
Execution halted
Packages required but not available:
  'caTools', 'tibble', 'dplyr', 'lubridate', 'magrittr', 'matlab',
  'plyr', 'readr', 'R.utils', 'signal', 'stringr', 'xts', 'dygraphs',
  'shiny', 'RColorBrewer', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'gridExtra', 'remotes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'lubridate', 'openxlsx'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'xfun'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'rgdal', 'sp', 'maxnet', 'dismo', 'ecospat', 'geosphere',
  'latticeExtra'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'qdap', 'dplyr', 'JWileymisc', 'tm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', '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: 'Iso', 'ggplot2', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
miney : plot.initial.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'text'
miney: no visible global function definition for 'locator'
miney: no visible global function definition for 'rect'
miney: no visible global function definition for 'title'
Undefined global functions or variables:
  locator rect text title
Consider adding
  importFrom("graphics", "locator", "rect", "text", "title")
to your NAMESPACE file.
Packages required but not available: 'httr', 'igraph', 'assertthat'

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'testthat', 'covr', 'withr',
  'mockery', 'testthis', 'roxygen2', 'mockr', '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:
  'htmltools', 'katex', 'knitr', 'mime', 'rmarkdown', 'sass', 'xfun'

Packages suggested but not available for checking:
  'callr', 'dplyr', 'purrr', 'shiny', 'testthat', 'tidyr', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'randtoolbox', 'DiceDesign', 'MaxPro', 'doParallel',
  'doSNOW', 'gtools', 'nloptr', 'foreach', 'jpeg', 'gmp',
  'conf.design', 'pdist', 'DoE.base', 'FrF2', 'geometry',
  'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'meta', 'shiny', 'shinyjs', 'shinyWidgets', 'colourpicker',
  'rhandsontable', 'metafor', 'markdown', 'WriteXLS', 'readxl',
  'jsonlite'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'htmltools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BiocParallel'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'pkgdown', 'seqinr', 'Biostrings', '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: 'glasso', 'trust', 'testthat'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'sybil', 'glpkAPI'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
minxent.multiple: no visible global function definition for 'cov.wt'
minxent.single: no visible global function definition for 'optimize'
Undefined global functions or variables:
  cov.wt optimize
Consider adding
  importFrom("stats", "cov.wt", "optimize")
to your NAMESPACE file.
Packages required but not available: 'cmm', 'Rsolnp', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doBy', 'gdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'stringr', 'tidyr', 'shinyWidgets', 'data.table',
  'readxl', 'shiny.i18n', 'showtextdb', 'shinyalert', 'readr',
  'showtext', 'shiny', 'reshape', 'rlang', 'dplyr', 'reshape2'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.FCLoess: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'median'
.Import.Luminex: no visible global function definition for 'read.csv'
.Intra.Me: no visible global function definition for 'sd'
.Intra.Me: no visible global function definition for 'quantile'
.Intra.Me: no visible global function definition for 'qchisq'
.Intra.Median: no visible global function definition for 'median'
.boxplot.rtprofile: no visible global function definition for 'boxplot'
.denplot: no visible global function definition for 'density'
.denplot: no visible global function definition for 'abline'
.normalize.Luminex: no visible global function definition for 'sd'
.normalize.qrtpcr: no visible global function definition for 'density'
.validate.default: no visible global function definition for 't.test'
Undefined global functions or variables:
  abline boxplot density loess median qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package required but not available: 'nanonext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'arm'

Packages suggested but not available for checking:
  'betareg', 'knitr', 'sn', 'truncnorm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'COMPoissonReg', 'matrixStats', 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'Formula', 'mvtnorm',
  'dirichletprocess', 'truncnorm', 'pracma', 'cubature', 'logspline',
  'HDInterval', 'BH', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'magrittr', 'openxlsx', 'plotly',
  'purrr', 'readr', 'readxl', 'rlang', 'scales', 'stringr',
  'textclean', 'tidyr', 'tidytext', 'topicmodels', 'wordcloud', 'xml2',
  'zoo'

Packages suggested but not available for checking:
  'kableExtra', 'knitr', 'reshape2', 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CompQuadForm', 'quantreg', 'GUniFrac', 'PearsonDS', 'lme4',
  'permute', 'mixtools'

Packages suggested but not available for checking:
  'knitr', 'propr', 'dirmult', 'vegan', 'rmarkdown', 'tidyverse',
  'kableExtra'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'pROC'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'CORElearn', 'RSpectra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mirt', 'shiny', 'Rcpp', 'markdown', 'pbapply', 'lpSolve',
  'RcppArmadillo'

Packages suggested but not available for checking: 'shinythemes', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'corpcor', 'globaltest', 'GlobalAncova', 'limma', 'RepeatedHighDim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'GPArotation', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GPArotation', 'gridExtra', 'Rcpp', 'vegan', 'Deriv', 'pbapply',
  'dcurver', 'RcppArmadillo'

Packages suggested but not available for checking:
  'latticeExtra', 'directlabels', 'shiny', 'knitr', 'markdown',
  'Rsolnp', 'nloptr', 'sirt', 'plink', 'mirtCAT'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GPArotation', 'mirtjml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'norm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mice'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rgl', 'tkrplot'
Packages unavailable to check Rd xrefs: 'rgl', 'scatterplot3d'
Running examples in 'misc3d-Ex.R' failed
The error most likely occurred in:

> ### Name: contour3d
> ### Title: Draw an Isosurface, a Three Dimension Contour Plot
> ### Aliases: contour3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: Draw a ball
>   f <- function(x, y, z)x^2+y^2+z^2
>   x <- seq(-2,2,len=20)
>   contour3d(f,4,x,x,x)
Error in loadRGL() : rgl is mot available
Calls: contour3d -> drawScene.rgl -> loadRGL
Execution halted
Packages required but not available: 'R2jags', 'MCMCpack', 'mvtnorm'

Packages suggested but not available for checking: 'mixAK', 'BRugs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'roxygen2', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nnls'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ucminf', 'numDeriv', 'bigmemory', 'foreach', 'mlogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'data.table', 'devtools', 'ggplot2', 'gridExtra', 'Rcpp', 'xtable'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'stringr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'digest'

Package suggested but not available for checking: 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'mice', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'forrel', 'pedtools', 'plotly', 'dplyr', 'highcharter', 'tidyr',
  'tidyverse', 'DirichletReg', 'purrr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'e1071', 'penalized'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'vegan', 'ape', 'aSPU', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'ade4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mixtools', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'numDeriv', 'VGAM', 'mvtnorm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Amelia', 'data.table', 'dplyr', 'ggdendro', 'ggplot2', 'Hmisc',
  'ltm', 'magrittr', 'mi', 'mice', 'missForest', 'missMDA',
  'pcaMethods', 'plyr', 'rlang', 'tidyr', 'VIM'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rms', 'relsurv', 'cmprsk', 'Rcpp', 'mitools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'cobalt'

Packages suggested but not available for checking: 'mice', 'sbw', 'ebal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randomForest', 'foreach', 'itertools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mcmcplots', 'ggpubr', 'ggmcmc', 'ggthemes', 'BCEA', 'ggplot2',
  'gridExtra', 'bayesplot', 'R2jags', 'loo', 'coda', 'mcmcr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FactoMineR', 'ggplot2', 'mice', 'mvtnorm', 'doParallel', 'foreach'

Packages suggested but not available for checking: 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'lpSolve', 'mvtnorm', 'norm', 'rmarkdown',
  'testthat', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'norm'
Running examples in 'missMethods-Ex.R' failed
The error most likely occurred in:

> ### Name: impute_EM
> ### Title: EM imputation
> ### Aliases: impute_EM
> 
> ### ** Examples
> 
> ds_orig <- mvtnorm::rmvnorm(100, rep(0, 7))
Error in loadNamespace(x) : there is no package called 'mvtnorm'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ranger', 'FNN'

Packages suggested but not available for checking:
  'dplyr', 'mice', 'rmarkdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'igraph', 'nloptr', 'ggplot2', 'future.apply', 'R6', 'rlang',
  'sbm', 'magrittr', 'RSpectra', 'RcppArmadillo'

Packages suggested but not available for checking:
  'aricode', 'blockmodels', 'corrplot', 'future', 'testthat', 'covr',
  'knitr', 'rmarkdown', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'kpodclustr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'e1071', 'mvtnorm', 'AcceptanceSampling', 'car', 'Dodge', 'tseries',
  'qcc', 'DoE.base', 'FrF2', 'rsm', 'LearnBayes', 'ggplot2',
  'DiceEval', 'DiceKriging', 'DiceDesign', 'DiceView', 'lhs',
  'fdapace', 'randomForest', 'xgboost'
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: 'qcc', 'AcceptanceSampling', 'FrF2'
Running examples in 'mistat-Ex.R' failed
The error most likely occurred in:

> ### Name: CONTACTLEN
> ### Title: Length of the Electrical Contacts
> ### Aliases: CONTACTLEN
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(CONTACTLEN)
> 
> library(qcc)
Error in library(qcc) : there is no package called 'qcc'
Execution halted
Packages required but not available:
  'e1071', 'mvtnorm', 'ggplot2', 'doParallel', 'foreach', 'iterators',
  'DiceKriging', 'emoa', 'quadprog', 'Rcpp'

Packages suggested but not available for checking:
  'microbenchmark', 'deSolve', 'scatterplot3d', 'KrigInv', 'rgenoud',
  'kernlab', 'knitr', 'rmarkdown', 'markdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CompQuadForm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'bbmle'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'rmarkdown', 'pinp'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'haven', 'lavaan', 'lme4', 'norm', 'r2mlm', 'readxl',
  'writexl'

Packages suggested but not available for checking: 'mnormt', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pan', 'jomo', 'haven'

Packages suggested but not available for checking:
  'mice', 'miceadds', 'Amelia', 'lme4', 'lavaan', 'geepack', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Biostrings', 'circlize', 'ComplexHeatmap', 'dynamicTreeCut',
  'GenomicRanges', 'ggplot2', 'gridExtra', 'IRanges', 'magrittr',
  'mcclust', 'rdist', 'reshape2', 'rlist', 'Rsamtools'

Packages suggested but not available for checking:
  'clustree', 'fmsb', 'gam', 'karyoploteR', 'knitr', 'plotly',
  'regioneR', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DBI'

Package suggested but not available for checking: 'RODBC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'plyr', 'dplyr', 'igraph', 'stringr', 'jsonlite', 'RJSONIO',
  'tidyr'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'stabledist'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'animation', 'magrittr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'magrittr', 'mice'

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:
  'coda', 'condMVNorm', 'ggplot2', 'glm2', 'Hmisc', 'invgamma',
  'matrixNormal', 'MCMCpack', 'mvtnorm', 'purrr', 'rlist', 'Rsolnp',
  'tidyr', 'tmvmixnorm', 'tmvtnorm', 'truncnorm'

Packages suggested but not available for checking:
  'formatR', 'GGally', 'knitr', 'mice', 'norm', 'pander', 'rmarkdown',
  'scales', 'sessioninfo', 'spelling', 'testthat', 'wqs'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colorspace', 'lme4', 'fastGHQuad', 'mnormt', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rtkore', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BB', 'combinat', 'timeDate', 'fGarch', 'Rdpack', 'gbutils',
  'MCMCpack', 'e1071', 'permute', 'mvtnorm'

Packages suggested but not available for checking:
  'fma', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'minpack.lm', 'nloptr', 'zoo', 'tmvtnorm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'expm', 'matrixcalc', 'Rsolnp', 'kdensity'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'flexsurv', 'survey', 'gam', 'timereg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'extraDistr', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'purrr', 'dplyr', 'rmutil', 'pheatmap',
  'mcclust', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'pcaPP', 'fMultivar', 'mnormt', 'irlba', 'chebpol',
  'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'fda', 'RcppProgress', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rmarkdown', 'ordinalClust', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'foreach', 'copula', 'ggplot2', 'survey'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'gtools', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking: 'knitr', 'xtable'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/mixedMem.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gaussquad', 'Rmpfr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'beepr', 'brglm', 'lme4', 'mnormt', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sde', 'moments', 'plot3D'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gdata', 'daewr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'mvtnorm', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RColorBrewer', 'fftw', 'MixSim', 'EMCluster'

Packages which this enhances but not available for checking:
  'pbdMPI', 'AnalyzeFMRI', 'oro.nifti'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Bessel', 'mvtnorm', 'ghyp', 'numDeriv', 'mixture', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mixOmics', 'ggplot2', 'reticulate', 'vegan', 'phyloseq', 'corrplot',
  'psych', 'quadprog', 'LDRTools', 'markdown'

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:
  'car', 'pls', 'multcomp', 'pracma', 'leaps'

Package suggested but not available for checking: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'maxLik', 'numDeriv', 'randtoolbox', 'Rcpp', 'readr', 'sandwich',
  'stringr'

Packages suggested but not available for checking:
  'knitr', 'mlogit', 'rmarkdown', 'testthat', 'texreg', 'xtable'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CholWishart', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'ggplot2', 'dplyr',
  'magrittr', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'metafor', 'meta', 'rmeta', 'dosresmeta', 'dlnm'
Packages unavailable to check Rd xrefs: 'metafor', 'mvmeta', 'dosresmeta'
Running examples in 'mixmeta-Ex.R' failed
The error most likely occurred in:

> ### Name: alcohol
> ### Title: Alcohol Intake and Colorectal Cancer
> ### Aliases: alcohol
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ### REPRODUCE THE RESULTS IN CRIPPA ET AL (2016) AND ORSINI ET AL (2012)
> 
> # LOAD THE PACKAGE dosresmeta AND splines
> library(dosresmeta) ; library(splines)
Error in library(dosresmeta) : there is no package called 'dosresmeta'
Execution halted
Packages required but not available:
  'ggplot2', 'patchwork', 'desirability', 'rlang'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pbapply', 'Formula', 'Rfast', 'dplyr', 'gamlss.dist', 'generics',
  'ggplot2', 'gridExtra', 'lmtest', 'magrittr', 'statmod', 'tibble',
  'rlang', 'ggrepel', 'gamlss'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'devtools', 'bbreg', 'testthat', 'covr',
  'tidyr', 'ggfortify', 'broom'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mixRasch', 'testthat'
Packages required but not available:
  'doParallel', 'randomForest', 'lme4', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'Rcpp'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat', '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: 'tcltk2', 'RODBC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'R2jags', 'RColorBrewer', 'reshape', 'reshape2',
  'MCMCpack', 'ggmcmc', 'coda', 'loo', 'bayesplot', 'splancs'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'mclust'
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'irlba', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'REBayes', 'Rmosek', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
fit.mixtNB: no visible global function definition for 'dnbinom'
fit.mixtNB: no visible global function definition for 'nlminb'
wald.test: no visible global function definition for 'pnorm'
wald.test: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
Packages required but not available: 'kernlab', 'segmented'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'minpack.lm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quadprog'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ContaminatedMixt', 'mvtnorm', 'mnormt', 'rootSolve'

Package suggested but not available for checking: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'BH', 'RcppGSL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'rlang', 'tidyr', 'RColorBrewer'

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: 'alabama', 'ashr', 'fdrtool', 'Iso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'assertthat', 'deSolve', 'dplyr', 'ggplot2', 'ggrepel', 'lubridate',
  'plotly', 'plyr', 'progress', 'Rcpp', 'reshape2', 'rlang',
  'lifecycle'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'roxygen2', 'knitr', 'shinyBS', 'rmarkdown',
  'pkgdown', 'covr', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'foreach', 'doParallel'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'rms'
Packages required but not available: 'Rcpp', 'raster', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'scales'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MKdescr', 'arrangements', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Amelia', 'exactRankTests'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'R6', 'inline', 'numDeriv', 'lmtest', 'pkgbuild', 'purrr',
  'saemix'

Packages suggested but not available for checking:
  'knitr', 'rbenchmark', 'tikzDevice', 'testthat', 'rmarkdown', 'covr',
  'vdiffr', 'benchmarkme', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
mkle: no visible global function definition for 'sd'
mkle: no visible global function definition for 'density'
mkle: no visible global function definition for 'optimize'
mkle.ci: no visible global function definition for 'sd'
mkle.ci: no visible binding for global variable 'var'
mkle.ci: no visible global function definition for 'quantile'
mkle.ci: no visible global function definition for 'qnorm'
opt.bw: no visible global function definition for 'sd'
opt.bw : mse: no visible global function definition for 'var'
opt.bw: no visible global function definition for 'optimize'
opt.bw: no visible global function definition for 'var'
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
Packages required but not available:
  'RColorBrewer', 'robustbase', 'ggplot2', 'scales', 'limma'

Packages suggested but not available for checking:
  'gplots', 'Amelia', 'knitr', 'rmarkdown', 'exactRankTests',
  'foreach', 'doParallel'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'assertthat', 'data.table', 'lpSolve'

Packages suggested but not available for checking:
  'testthat', 'mockery', 'Rglpk', 'ROI', 'ROI.plugin.glpk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RColorBrewer', 'robustbase', 'limma', 'circlize', 'ComplexHeatmap'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'matrixTests', 'ggplot2', 'MKdescr', 'MKinfer', 'qqplotr', 'coin'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'keras', 'reticulate', 'tensorflow', 'tfprobability'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'R6'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'limSolve', 'MultiLCIRT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'klaR', 'dplyr', 'caret', 'DiscriMiner',
  'e1071', 'rhandsontable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'klaR', 'dplyr', 'caret', 'DiscriMiner',
  'e1071', 'rhandsontable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ConfusionTableR', 'dplyr', 'parsnip', 'rsample', 'recipes',
  'workflows', 'ranger', 'caret', 'varhandle', 'OddsPlotty', 'ggplot2'

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.
Package suggested but not available for checking: 'mldr'
Packages required but not available: 'shiny', 'XML', 'circlize'

Packages suggested but not available for checking:
  'pROC', 'knitr', 'mldr.datasets', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/mldr.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'e1071', 'randomForest', 'ipred'

Packages suggested but not available for checking:
  'mlbench', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plotCDF1: no visible global function definition for 'lines'
plotCDF2: no visible global function definition for 'gray'
plotCDF2: no visible global function definition for 'image'
plotCDF2: no visible global function definition for 'box'
plotCDF2: no visible global function definition for 'par'
plotCDF2: no visible global function definition for 'rect'
plotCDF2: no visible global function definition for 'text'
plotCM: no visible global function definition for 'image'
plotCM: no visible global function definition for 'axis'
plotCM: no visible global function definition for 'box'
plotDens1: no visible global function definition for 'lines'
plotDens2: no visible global function definition for 'gray'
plotDens2: no visible global function definition for 'rect'
plotDens2: no visible global function definition for 'axis'
plotDens2: no visible global function definition for 'text'
plotHM: no visible global function definition for 'terrain.colors'
plotHM: no visible global function definition for 'image'
plotHM: no visible global function definition for 'box'
plotHM: no visible global function definition for 'abline'
plotHM: no visible global function definition for 'text'
plotHM: no visible global function definition for 'par'
plotHM: no visible global function definition for 'rect'
plotRects: no visible global function definition for 'rainbow'
plotRects: no visible global function definition for 'abline'
plotRects: no visible global function definition for 'rect'
Undefined global functions or variables:
  abline axis box gray image lines par rainbow rect terrain.colors text
Consider adding
  importFrom("grDevices", "gray", "rainbow", "terrain.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "lines",
             "par", "rect", "text")
to your NAMESPACE file.
Package suggested but not available for checking: 'snowfall'
Packages required but not available:
  'ergm', 'network', 'stringr', 'GGally', 'ggplot2', 'cowplot',
  'reshape2', 'plyr', 'lpSolve', 'sna'

Packages suggested but not available for checking:
  'RColorBrewer', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'fitdistrplus'
Running examples in 'mle.tools-Ex.R' failed
The error most likely occurred in:

> ### Name: coxsnell.bc
> ### Title: Bias-Corrected Maximum Likelihood Estimate(s)
> ### Aliases: coxsnell.bc
> 
> ### ** Examples
> 
> {library(mle.tools); library(fitdistrplus); set.seed(1)};
Error in library(fitdistrplus) : 
  there is no package called 'fitdistrplus'
Execution halted
Packages required but not available: 'urca', 'stabledist', 'fGarch'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BB', 'dplyr', 'hms', 'kimisc', 'plyr', 'tibble', 'forcats', 'rlang',
  'wrswoR', 'lifecycle'

Packages suggested but not available for checking:
  'covr', 'testthat', 'sampling', 'XML', 'waldo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'forge', 'fs', 'git2r', 'glue', 'httpuv', 'httr', 'ini',
  'jsonlite', 'openssl', 'processx', 'purrr', 'reticulate', 'rlang',
  'swagger', 'tibble', 'withr', 'yaml', 'zeallot'

Packages suggested but not available for checking:
  'carrier', 'covr', 'h2o', 'keras', 'lintr', 'sparklyr', 'stringi',
  'testthat', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'gglasso', 'fastcluster', 'FactoMineR', 'parallelDist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CheckStability: no visible global function definition for 'cor'
CheckStability: no visible global function definition for 'var'
PriorNormPCA: no visible global function definition for 'barplot'
SortModes: no visible global function definition for 'rnorm'
mlicaMAIN: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot cor rnorm runif var
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "rnorm", "runif", "var")
to your NAMESPACE file.
Package required but not available: 'lme4'

Packages suggested but not available for checking:
  'raster', 'sp', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'car', 'abind', 'coxme', 'gplots'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ROCR'

Package suggested but not available for checking: 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gsl', 'norm', 'cat', 'mix'

Packages suggested but not available for checking: 'bootImpute', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'minfi', 'microbenchmark', 'GEOquery', 'knitr', 'rmarkdown',
  'IlluminaHumanMethylation450kmanifest'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'multcompView', 'multcomp', 'coxme', 'sommer'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppDist'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'XLConnect', 'rJava', 'Rdpack', 'Rmpfr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'foreach'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'doParallel'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quantspec', 'waveslim', 'Rfast', 'TSclust', 'forecast', 'tseries',
  'TSA', 'tsfeatures', 'tseriesChaos', 'freqdom', 'e1071', 'dtw',
  'psych', 'complexplus', 'MTS', 'ggplot2', 'multiwave', 'fda.usc',
  'TSdist', 'evolqg', 'geigen', 'DescTools', 'pracma', 'pspline',
  'Rdpack', 'ClusterR', 'AID', 'caret', 'ranger'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BMA', 'abind', 'maxLik'

Package suggested but not available for checking: 'mlogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dfidx', 'Formula', 'zoo', 'lmtest', 'statmod', 'Rdpack'

Packages suggested but not available for checking:
  'knitr', 'car', 'AER', 'ggplot2', 'texreg', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'BH', 'RcppEnsmallen'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'progress', 'C50', 'randomForest'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'caret', 'randomForest', 'FNN'

Package suggested but not available for checking: 'CORElearn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'ggplot2', 'mlr3misc', 'R6'

Packages suggested but not available for checking:
  'mlr3', 'mlr3learners', 'PMCMRplus', 'testthat', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'backports', 'checkmate', 'clue', 'clusterCrit',
  'data.table', 'mlr3misc', 'paradox', 'R6'

Packages suggested but not available for checking:
  'dbscan', 'e1071', 'ClusterR', 'kernlab', 'apcluster', 'LPCM',
  'mlbench', 'RWeka', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mlr3'
Package unavailable to check Rd xrefs: 'palmerpenguins'
Packages required but not available:
  'mlr3', 'R6', 'backports', 'checkmate', 'data.table', 'mlr3misc'

Packages suggested but not available for checking:
  'DBI', 'RSQLite', 'dbplyr', 'dplyr', 'duckdb', 'future',
  'future.apply', 'future.callr', 'lgr', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'data.table', 'mlr3', 'mlr3misc',
  'paradox', 'R6'

Packages suggested but not available for checking:
  'care', 'caret', 'FSelectorRcpp', 'knitr', 'lgr', 'mlr3learners',
  'mlr3measures', 'praznik', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'bbotk', 'checkmate', 'data.table', 'lgr', 'mlr3misc',
  'mlr3pipelines', 'paradox', 'R6'

Packages suggested but not available for checking: 'genalg', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3tuning', 'bbotk', 'checkmate', 'data.table', 'lgr', 'mlr3',
  'mlr3misc', 'paradox', 'R6'

Packages suggested but not available for checking:
  'emoa', 'mlr3learners', 'mlr3pipelines', 'testthat', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'checkmate', 'data.table', 'mlr3misc', 'paradox', 'R6'

Packages suggested but not available for checking:
  'DiceKriging', 'distr6', 'e1071', 'glmnet', 'kknn', 'knitr', 'lgr',
  'mlr3proba', 'pracma', 'ranger', 'rgenoud', 'rmarkdown', 'testthat',
  'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'checkmate', 'PRROC'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'data.table', 'digest', 'R6'

Packages suggested but not available for checking:
  'callr', 'evaluate', 'paradox', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'curl', 'data.table', 'jsonlite', 'lgr',
  'mlr3', 'mlr3misc', 'R6', 'stringi'

Packages suggested but not available for checking:
  'RWeka', 'farff', 'mlr3proba', 'qs', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'data.table', 'digest', 'lgr', 'mlr3',
  'mlr3misc', 'paradox', 'R6', 'withr'

Packages suggested but not available for checking:
  'ggplot2', 'glmnet', 'igraph', 'knitr', 'lme4', 'mlbench', 'bbotk',
  'mlr3filters', 'mlr3learners', 'mlr3measures', 'nloptr', 'quanteda',
  'rmarkdown', 'stopwords', 'testthat', 'visNetwork', 'bestNormalize',
  'fastICA', 'kernlab', 'smotefamily', 'evaluate', 'NMF', 'kknn',
  'GenSA', 'vtreat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'checkmate', 'data.table', 'distr6', 'mlr3misc', 'paradox',
  'R6', 'Rcpp'

Packages suggested but not available for checking:
  'bujar', 'cubature', 'ggplot2', 'knitr', 'lgr', 'mlr3pipelines',
  'param6', 'pracma', 'set6', 'simsurv', 'survAUC', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'backports', 'checkmate', 'data.table', 'evaluate', 'future',
  'future.apply', 'lgr', 'mlbench', 'mlr3measures', 'mlr3misc',
  'parallelly', 'palmerpenguins', 'paradox', 'uuid'

Packages suggested but not available for checking:
  'callr', 'distr6', 'future.callr', 'mlr3data', 'progressr',
  'remotes', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'mlr3measures', 'mlr3learners', 'shiny', 'shinythemes',
  'shinydashboard', 'shinyjs', 'shinyWidgets', 'shinyalert',
  'data.table', 'DT', 'readxl', 'stringr', 'plyr', 'purrr', 'ranger',
  'e1071'

Packages suggested but not available for checking:
  'testthat', 'shinytest', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'checkmate', 'data.table', 'lgr', 'mlr3misc', 'R6', 'terra'

Packages suggested but not available for checking:
  'bench', 'e1071', 'future', 'future.callr', 'knitr', 'mlr3learners',
  'mlr3tuning', 'paradox', 'ranger', 'raster', 'rgdal', 'rmarkdown',
  'sf', 'stars', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'ggplot2', 'mlr3', 'mlr3misc', 'paradox',
  'R6'

Packages suggested but not available for checking:
  'bbotk', 'blockCV', 'caret', 'CAST', 'ggsci', 'ggtext', 'knitr',
  'lgr', 'mlr3filters', 'mlr3pipelines', 'mlr3tuning', 'patchwork',
  'plotly', 'raster', 'rgdal', 'rmarkdown', 'sf', 'skmeans',
  'sperrorest', 'testthat', 'vdiffr', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'paradox', 'bbotk', 'checkmate', 'data.table', 'lgr',
  'mlr3misc', 'R6'

Packages suggested but not available for checking:
  'adagio', 'GenSA', 'irace', 'mlr3pipelines', 'nloptr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3tuning', 'checkmate', 'data.table', 'mlr3', 'mlr3misc',
  'paradox', 'R6'

Packages suggested but not available for checking:
  'e1071', 'glmnet', 'kknn', 'mlr3learners', 'ranger', 'testthat',
  'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'bbotk', 'data.table', 'mlr3cluster', 'mlr3data',
  'mlr3filters', 'mlr3fselect', 'mlr3hyperband', 'mlr3learners',
  'mlr3misc', 'mlr3pipelines', 'mlr3proba', 'mlr3tuning',
  'mlr3tuningspaces', 'mlr3viz', 'paradox'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'ggplot2', 'mlr3misc'

Packages suggested but not available for checking:
  'bbotk', 'distr6', 'factoextra', 'GGally', 'ggfortify', 'ggparty',
  'glmnet', 'lgr', 'mlr3', 'mlr3cluster', 'mlr3filters',
  'mlr3learners', 'mlr3proba', 'mlr3tuning', 'paradox', 'partykit',
  'patchwork', 'precrec', 'ranger', 'testthat', 'vdiffr', 'xgboost'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ParamHelpers', 'mlr', 'BBmisc', 'stringi', 'checkmate', 'backports'

Packages suggested but not available for checking:
  'care', 'party', 'mlbench', 'knitr', 'rmarkdown', 'testthat',
  'mRMRe', 'praznik', 'randomForestSRC', 'randomForest', 'ranger',
  'Rfast', 'FSelector', 'FSelectorRcpp', 'e1071', 'DiscriMiner',
  'digest', 'lintr', 'Hmisc', 'fastICA', 'rex'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'data.table', 'mlr3misc', 'paradox', 'R6',
  'lhs', 'callr', 'bbotk', 'mlr3tuning'

Packages suggested but not available for checking:
  'mlr', 'ParamHelpers', 'testthat', 'rgenoud', 'DiceKriging', 'emoa',
  'cmaesr', 'randomForest', 'smoof', 'lgr', 'mlr3', 'mlr3learners',
  'mlr3pipelines', 'mlrMBO', 'ranger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr', 'ParamHelpers', 'smoof', 'backports', 'BBmisc', 'checkmate',
  'data.table', 'lhs', 'parallelMap'

Packages suggested but not available for checking:
  'akima', 'cmaesr', 'ggplot2', 'DiceKriging', 'earth', 'emoa',
  'GGally', 'gridExtra', 'kernlab', 'kknn', 'knitr', 'mco', 'party',
  'randomForest', 'reshape2', 'rmarkdown', 'rgenoud', 'testthat',
  'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ParamHelpers', 'backports', 'BBmisc', 'checkmate', 'data.table',
  'ggplot2', 'parallelMap', 'stringi', 'XML'

Packages suggested but not available for checking:
  'ada', 'adabag', 'bartMachine', 'batchtools', 'bit64', 'brnn', 'bst',
  'C50', 'care', 'caret', 'clue', 'ClusterR', 'clusterSim', 'cmaes',
  'cowplot', 'crs', 'Cubist', 'deepnet', 'DiceKriging', 'DiscriMiner',
  'e1071', 'earth', 'elasticnet', 'emoa', 'evtree', 'extraTrees',
  'fda.usc', 'FDboost', 'FNN', 'forecast', 'fpc', 'frbs', 'FSelector',
  'FSelectorRcpp', 'gbm', 'GenSA', 'ggpubr', 'glmnet', 'GPfit', 'h2o',
  'Hmisc', 'irace', 'kernlab', 'kknn', 'klaR', 'knitr', 'laGP',
  'LiblineaR', 'lintr', 'mboost', 'mco', 'mda', 'memoise', 'mlbench',
  'mldr', 'mlrMBO', 'mmpf', 'modeltools', 'mRMRe', 'neuralnet',
  'nodeHarvest', 'numDeriv', 'pamr', 'pander', 'party', 'pec',
  'penalized', 'pls', 'PMCMRplus', 'praznik', 'randomForest',
  'randomForestSRC', 'ranger', 'rappdirs', 'refund', 'rex', 'rFerns',
  'rgenoud', 'rknn', 'rmarkdown', 'Rmpi', 'ROCR', 'rotationForest',
  'RRF', 'rrlda', 'rsm', 'RSNNS', 'rucrdtw', 'RWeka', 'sda', 'sf',
  'smoof', 'snow', 'sparseLDA', 'stepPlr', 'survAUC', 'svglite',
  'SwarmSVM', 'testthat', 'tgp', 'TH.data', 'tidyr', 'tsfeatures',
  'vdiffr', 'wavelets', 'xgboost'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'mlt', 'numDeriv', 'eha', 'multcomp', 'flexsurv', 'truncreg', 'np'

Packages suggested but not available for checking:
  'variables', 'basefun', 'TH.data', 'knitr', 'prodlim', 'gridExtra',
  'HSAUR3', 'sandwich', 'latticeExtra', 'colorspace', 'coxinterval',
  'ICsurv', 'polspline', 'logspline', 'bshazard', 'gss', 'MIICD',
  'TransModel', 'dynsurv', 'timereg', 'survivalMPL', 'gamlss', 'muhaz',
  'ICE', 'ordinal', 'VGAM', 'AER', 'coin', 'gamlss.data', 'mlbench',
  'tram', 'rms'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/mlt.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'data.table'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'basefun', 'variables', 'BB', 'alabama', 'coneproj', 'sandwich',
  'numDeriv'

Packages suggested but not available for checking: 'TH.data', 'multcomp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'arm', 'qgraph', 'dplyr', 'clusterGeneration', 'mvtnorm',
  'corpcor', 'plyr', 'abind', 'MplusAutomation', 'graphicalVAR',
  'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'blockmodels', 'ape', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'ggplot2', 'tidygraph',
  'ggraph', 'ggforce', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'XML', 'Rcpp', 'reshape2', 'gridExtra', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'gplots', 'ggplot2', 'reshape2', 'TMB', 'RcppEigen'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Biobase'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/MM2Sdata.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GSVA', 'kknn', 'pheatmap'

Packages suggested but not available for checking: 'knitr', 'MM2Sdata'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/MM2S.Rnw'
   'inst/doc/MM2S_FromRawData.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'mma', 'car', 'gplots'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'mosaic', 'mosaicCalc', 'manipulate'
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'loder', 'tinytest', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'rmio'

Packages suggested but not available for checking: 'covr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'Cairo', 'xts', 'lubridate', 'zoo', 'caTools',
  'ggplot2', 'data.table', 'DT', 'dplyr', 'leaflet', 'stringr',
  'shiny', 'XML', 'shinyjs', 'plotly'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'usethis', 'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gbm', 'car', 'gplots'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rdpack', 'foreach', 'doParallel'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'covr', 'e1071', 'caret', 'knitr',
  'rmarkdown', 'ggplot2', 'ggpubr', 'cowplot', 'philentropy', 'Rtsne'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'VineCopula', 'cubature', 'pcaPP', 'randtoolbox', 'pbapply'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'e1071', 'plyr', 'bigmemory'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Biobase', 'lawstat'

Package suggested but not available for checking: 'ALL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jointDiag', 'lme4', 'matrixcalc', 'psych', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'aod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gee'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

Packages suggested but not available for checking: 'geepack', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'adegenet', 'pegas'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'checkmate', 'data.table'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr', 'randomForest', 'ggplot2',
  'reshape2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Oarray', 'partitions', 'magic', 'abind', 'emulator', 'mathjaxr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'reshape', 'reshape2', 'ggplot2', 'rlang', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'sn', 'rmutil', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'flexsurv', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'dplyr', 'tibble', 'stringi', 'Rcpp', 'janitor',
  'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'CDM', 'Rcpp', 'RcppArmadillo'

Packages which this enhances but not available for checking:
  'aMNLFA', 'GPCMlasso', 'sirt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'magrittr', 'ggplot2', 'scales'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'shiny', 'rmarkdown', 'e1071', 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ICSNP', 'SpatialNP', 'ellipse', 'ICS'

Packages suggested but not available for checking:
  'Flury', 'gamlss', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'semTools'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'tmvnsim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'glmnet', 'mvtnorm', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'knitr', 'kableExtra', 'ggplot2', 'XML', 'plyr', 'yaml',
  'mailR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'texmex', 'copBasic', 'ks', 'SpatialExtremes', 'zoo', 'copula',
  'ggplot2', 'viridis'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'EMMREML', 'BGLR', 'doMPI', 'doRNG', 'foreach', 'sommer', 'vcfR',
  'jsonlite', 'rrBLUP', 'biomaRt', 'doParallel', 'RColorBrewer',
  'optiSel', 'alstructure', 'NAM', 'gplots', 'phylogram', 'cPCG'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Running examples in 'MoBPS-Ex.R' failed
The error most likely occurred in:

> ### Name: get.dendrogram
> ### Title: Dendrogram
> ### Aliases: get.dendrogram
> 
> ### ** Examples
> 
> data(ex_pop)
> get.dendrogram(ex_pop, gen=2)
Error in get.dendrogram(ex_pop, gen = 2) : object 'geno_dend' not found
Execution halted
Packages required but not available: 'gbm', 'Rborist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plotrix', 'scales', 'dplyr', 'purrr', 'tidyr', 'pbapply', 'ggplot2',
  'egg', 'tibble', 'vctrs', 'rlang', 'geosphere'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cclust', 'clue'

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', 'R6', '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: 'lazyeval'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'pkgload', 'curl', 'jsonlite', 'withr'
Packages unavailable to check Rd xrefs: 'testthat', 'withr'
Running examples in 'mockthat-Ex.R' failed
The error most likely occurred in:

> ### Name: mock
> ### Title: Mocking helper functions
> ### Aliases: mock mock_call mock_args mock_arg mock_n_called
> 
> ### ** Examples
> 
> url <- "https://eu.httpbin.org/get?foo=123"
> 
> mk <- mock("mocked request")
> dl <- function(x) curl::curl(x)
> 
> with_mock(`curl::curl` = mk, dl(url))
Error in loadNamespace(name) : there is no package called 'curl'
Calls: with_mock ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mvtnorm', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DT', 'RColorBrewer', 'collapsibleTree', 'dplyr', 'dygraphs',
  'highcharter', 'jsonlite', 'lazyeval', 'leaflet', 'networkD3',
  'plotly', 'rgdal', 'shiny', 'shinyBS', 'shinydashboard',
  'shinydashboardPlus', 'sp', 'sparkline', 'sunburstR', 'treemap',
  'htmlwidgets', 'magrittr'

Package suggested but not available for checking: 'modgetxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fBasics', 'stable', 'stabledist', 'statip'

Packages suggested but not available for checking:
  'evd', 'knitr', 'mvtnorm', 'testthat', 'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'partykit', 'sandwich', 'ggplot2', 'Formula', 'gridExtra'

Packages suggested but not available for checking:
  'mvtnorm', 'TH.data', 'psychotools', 'strucchange', 'plyr', 'knitr',
  'ggbeeswarm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bayestestR', 'effectsize', 'insight', 'datawizard', 'parameters',
  'performance'

Packages suggested but not available for checking:
  'brms', 'coda', 'correlation', 'dplyr', 'emmeans', 'forcats',
  'gamm4', 'gganimate', 'ggplot2', 'glmmTMB', 'knitr', 'lme4',
  'logspline', 'marginaleffects', 'merTools', 'patchwork', 'rmarkdown',
  'rstanarm', 'rtdists', 'see', 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: 'covr'
Note: found 313 marked UTF-8 strings
Packages required but not available:
  'dplyr', 'rlang', 'purrr', 'tibble', 'progress', 'ggplot2',
  'tidypredict'

Packages suggested but not available for checking:
  'dbplyr', 'testthat', 'knitr', 'rmarkdown', 'nycflights13',
  'RSQLite', 'DBI', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DALEX', 'auditor', 'ggplot2', 'whisker', 'DT', 'kableExtra',
  'psych', 'archivist', 'svglite', 'devtools', 'breakDown', 'drifter'

Packages suggested but not available for checking:
  'ranger', 'testthat', 'useful'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ClassDiscovery', 'ClassComparison', 'oompaBase', 'TailRank',
  'e1071', 'randomForest', 'neuralnet'

Package suggested but not available for checking: 'Biobase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'PolynomF', 'SparseM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'prodlim'

Packages suggested but not available for checking:
  'party', 'glmnet', 'rms', 'randomForest', 'randomForestSRC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'purrr', 'dplyr', 'magrittr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'recipes', 'randomForest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quantreg', 'coxrobust', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'randomForest', 'raster', 'rgdal', 'corrplot', 'fields',
  'HandTill2001', 'PresenceAbsence'

Packages suggested but not available for checking:
  'party', 'quantregForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'Rcpp', '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:
  'ggplot2', 'gridExtra', 'magrittr', 'dplyr', 'RColorBrewer',
  'ggfittext', 'scales', 'rlang'

Packages suggested but not available for checking:
  'mlr', 'caret', 'randomForest', 'e1071', 'h2o', 'keras', 'knitr',
  'rmarkdown', 'testthat', 'xgboost', 'stringr', 'kableExtra',
  'ranger', 'glmnet'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'do', 'tmcn', 'ROCit', 'survivalROC'

Packages suggested but not available for checking: 'ggDCA', 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'magrittr', 'purrr', 'rlang', 'tibble', 'tidyr',
  'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DALEX', 'ingredients', 'iBreakDown', 'r2d3', 'jsonlite', 'progress',
  'digest'

Packages suggested but not available for checking:
  'parallelMap', 'ranger', 'xgboost', 'knitr', 'rmarkdown', 'testthat',
  'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'checkmate', 'generics', 'glue', 'insight', 'kableExtra',
  'parameters', 'performance', 'rlang', 'tables'

Packages suggested but not available for checking:
  'betareg', 'bookdown', 'broom.mixed', 'covr', 'digest', 'DT',
  'estimatr', 'fixest', 'flextable', 'gamlss', 'ggplot2', 'gt',
  'huxtable', 'IRdisplay', 'knitr', 'lfe', 'lme4', 'lmtest', 'magick',
  'officer', 'rmarkdown', 'sandwich', 'spelling', 'testthat', 'tibble',
  'mice', 'pscl', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'generics', 'purrr', 'testthat', 'tibble'

Package suggested but not available for checking: 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'modeltime', 'modeltime.resample', 'tune', 'rsample', 'yardstick',
  'workflows', 'parsnip', 'recipes', 'timetk', 'tibble', 'dplyr',
  'tidyr', 'purrr', 'glue', 'stringr', 'rlang', 'cli', 'generics',
  'magrittr', 'tictoc', 'doParallel', 'foreach'

Packages suggested but not available for checking:
  'gt', 'crayon', 'dials', 'glmnet', 'progressr', 'roxygen2', 'earth',
  'testthat', 'tidymodels', 'xgboost', 'tidyverse', 'lubridate',
  'knitr', 'rmarkdown', 'covr', 'qpdf', 'remotes'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'modeltime', 'parsnip', 'timetk', 'magrittr', 'rlang', 'reticulate',
  'tibble', 'forcats', 'dplyr', 'tidyr', 'purrr', 'stringr', 'glue',
  'fs'

Packages suggested but not available for checking:
  'tidyverse', 'tidymodels', 'knitr', 'rmarkdown', 'roxygen2',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'modeltime', 'h2o', 'magrittr', 'rlang', 'tibble', 'timetk', 'dplyr',
  'parsnip', 'purrr', 'tidyr', 'stringr', 'glue', 'fs'

Packages suggested but not available for checking:
  'tidymodels', 'workflows', 'tidyverse', 'knitr', 'rmarkdown',
  'roxygen2', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'StanHeaders', 'timetk', 'parsnip', 'dials', 'yardstick',
  'workflows', 'hardhat', 'rlang', 'glue', 'plotly', 'reactable', 'gt',
  'ggplot2', 'tibble', 'tidyr', 'dplyr', 'purrr', 'stringr', 'forcats',
  'scales', 'janitor', 'doParallel', 'foreach', 'magrittr', 'forecast',
  'xgboost', 'prophet', 'cli'

Packages suggested but not available for checking:
  'rstan', 'slider', 'sparklyr', 'tidymodels', 'workflowsets',
  'recipes', 'rsample', 'tune', 'tidyverse', 'lubridate', 'progress',
  'testthat', 'roxygen2', 'kernlab', 'glmnet', 'thief', 'smooth',
  'greybox', 'earth', 'randomForest', 'tidyquant', 'knitr',
  'rmarkdown', 'webshot', 'qpdf', 'covr', 'TSrepr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'modeltime', 'tune', 'rsample', 'workflows', 'parsnip', 'recipes',
  'dials', 'yardstick', 'timetk', 'tibble', 'dplyr', 'tidyr', 'purrr',
  'forcats', 'glue', 'stringr', 'ggplot2', 'plotly', 'cli', 'crayon',
  'magrittr', 'rlang', 'progressr', 'tictoc'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'tidymodels', 'tidyverse', 'tidyquant',
  'glmnet', 'lubridate', 'knitr', 'rmarkdown', 'covr', 'remotes'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'magrittr', 'dplyr', 'ggplot2', 'tibble', 'janitor', 'broom',
  'formula.tools', 'stringr', 'knitr', 'infer', 'rlang', 'glue'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown', 'vdiffr', 'openintro', 'patchwork',
  'viridis', 'readr', 'nycflights13'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'markovchain', 'Rcpp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'rhandsontable', 'shiny', 'shinyBS'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'DT', 'shinydashboard', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'markdown', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'norm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'date', 'sp', 'sfsmisc', 'raster', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'RCurl', 'lubridate', 'gdalUtils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'sf', 'raster', 'memoise', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'testthat', 'rgdal', 'ggplot2', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'bitops', 'data.table', 'gdalUtilities', 'geojsonio',
  'httr', 'jsonlite', 'raster', 'sf', 'stringr', 'xml2', 'xts'

Packages suggested but not available for checking:
  'dplyr', 'DT', 'formatR', 'geojsonlint', 'ggplot2', 'httptest',
  'knitr', 'leafem', 'leaflet', 'magrittr', 'mapedit', 'png',
  'rappdirs', 'rgdal', 'rmarkdown', 'shiny', 'shinyalert',
  'shinydashboard', 'shinyFiles', 'shinyjs', 'spelling', 'testthat',
  'tibble', 'tidyr', 'xtable'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'sandwich', 'AER'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'AER'
Running examples in 'modmarg-Ex.R' failed
The error most likely occurred in:

> ### Name: marg.ivreg
> ### Title: Predicted Margins for 'ivreg' objects from the 'AER' package
> ### Aliases: marg.ivreg
> 
> ### ** Examples
> 
> # From ?AER::ivreg
> 
> # data
> data("CigarettesSW", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'gtools', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'corpcor', 'ggplot2', 'glinternet', 'glmnet', 'gridExtra',
  'gtools', 'igraph', 'interactionTest', 'leaps', 'lme4', 'lmerTest',
  'mvtnorm', 'pbapply', 'plyr', 'psych', 'qgraph', 'reshape2',
  'systemfit'

Packages suggested but not available for checking:
  'sn', 'arm', 'hierNet', 'psychTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ROI', 'ROI.plugin.glpk', 'ROI.plugin.quadprog'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lpSolve', 'geometry'

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'jmuOutlier', 'ellipse', 'hypergeo', 'gsl'

Packages suggested but not available for checking: 'BioStatR', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DescTools', 'e1071', 'C50', 'randomForest', 'pROC', 'pscl',
  'relaimpo', 'rpart.plot', 'lmtest', 'car', 'robustbase',
  'NeuralNetTools', 'naivebayes', 'sandwich', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'impute', 'dynamicTreeCut'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'devtools', 'knitr', 'lintr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'FNN', 'assertthat'

Packages suggested but not available for checking:
  'smoof', 'scatterplot3d', 'irace', 'testthat', 'knitr', 'rmarkdown',
  'emoa', 'ggplot2', 'reshape2', 'pkgdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'matrixStats', 'mclust', 'mvnfast', 'vcd'

Packages suggested but not available for checking:
  'clustMD', 'geometry', 'knitr', 'rmarkdown', 'snow'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'glue', 'purrr', 'httr', 'jsonlite', 'tibble', 'readr',
  'rlang', 'stringr', 'assertthat', 'cli', 'dplyr', 'lubridate'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'VGAM', 'tolerance'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cvTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RJSONIO', 'magrittr', 'tidyr', 'iterators', 'stringr', 'compareDF'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'poLCA', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DiceKriging', 'GenSA', 'emoa', 'mco', 'GPareto'

Packages suggested but not available for checking: 'knitr', 'lhs'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'alphahull', 'rgl', 'Rvcg'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rglwidget'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'urltools', 'xml2', 'aws.iam', 'aws.s3', 'MolgenisAuth',
  'arrow'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'mockery', 'tibble', 'rmarkdown',
  'DSMolgenisArmadillo'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'urltools'

Packages suggested but not available for checking: 'testthat', 'mockery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'arrangements'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'doParallel', 'foreach', 'ggplot2', 'ggridges', 'ess'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pander', 'dplyr', 'testthat', 'igraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'dplyr', 'stringr', 'WGCNA', 'Rfast', 'readr', 'tibble',
  'tidyr', 'magrittr', 'rlang'

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:
  'mvtnorm', 'ncvreg', 'Rcpp', 'mclust', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'patrick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'sandwich'

Packages suggested but not available for checking:
  'lmtest', 'knitr', 'texreg'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/gelS4.Rnw'
   'inst/doc/gmmS4.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
agostino.test: no visible global function definition for
  'complete.cases'
agostino.test: no visible global function definition for 'pnorm'
anscombe.test: no visible global function definition for
  'complete.cases'
anscombe.test: no visible global function definition for 'pnorm'
bonett.test: no visible global function definition for 'complete.cases'
bonett.test: no visible global function definition for 'pnorm'
jarque.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'doParallel', 'foreach', 'numDeriv', 'CircStats', 'crawl',
  'mvtnorm', 'sp', 'Brobdingnag', 'doRNG', 'rlang', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'setRNG', 'splines2', 'R.rsp', 'raster', 'conicfit',
  'ggplot2', 'ggmap', 'lubridate', 'dplyr', 'magrittr',
  'scatterplot3d', 'BB', 'expm', 'matrixcalc', 'moveHMM', 'extraDistr',
  'data.tree', 'geosphere', 'mitools', 'doFuture', 'future', 'car',
  'prodlim', 'nleqslv', 'qdapRegex'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dendextend', 'dplyr', 'magrittr', 'geometry', 'geomorph', 'ggplot2',
  'jpeg', 'progress', 'RColorBrewer', 'rgeos', 'sp', 'vegan', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'testthat', 'covr', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'topicmodels', 'tm', 'slam', 'magrittr', 'dplyr', 'doParallel',
  'foreach'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'markdown', 'rmarkdown', 'aricode', 'ggplot2',
  'tidytext', 'reshape2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'gplots', 'nortest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'mvtnorm', 'tlrmvnmvt', 'hypergeo', 'RcppArmadillo'

Packages suggested but not available for checking: 'TTmoment', 'tmvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmlwidgets', 'rstudioapi', 'htmltools', 'shiny'

Package suggested but not available for checking: 'sass'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvest', 'httr', 'magrittr', 'rlang', 'xml2', 'glue', 'lifecycle',
  'purrr'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'zoo'
Package unavailable to check Rd xrefs: 'zoo'
Package required but not available: 'RColorBrewer'

Packages suggested but not available for checking: 'DT', 'shiny', 'shinyBS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DBI', 'digest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jsonlite', 'openssl', 'mime'

Packages suggested but not available for checking:
  'spelling', 'nycflights13', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'jsonlite', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'mongolite', 'nycflights13'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tuneR'

Packages suggested but not available for checking: 'fftw', 'RODBC', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/monitoR_QuickStart.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'optimx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DT', 'monobin', 'shiny', 'shinydashboard', 'shinyjs', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'dplyr', 'foreach', 'ggplot2', 'permute', 'purrr',
  'rlang', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'mice', 'rmarkdown', 'covr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'maptools', 'circular', 'png', 'raster', 'rmarkdown', 'sp'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'compare', 'doParallel', 'foreach', 'iterators', 'sitar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pls', 'lars', 'quadprog', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'phytools', 'phangorn', 'RColorBrewer', 'taxize'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'paleotree', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quadprog'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lmtest', 'sandwich'

Packages suggested but not available for checking: 'testthat', 'xts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'snow', 'abind', 'rlecuyer', 'snowfall', 'reshape'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'dplyr', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lavaan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DBI', 'dplyr', 'ggplot2', 'tidytext', 'ggwordcloud', 'stringr',
  'rlang', 'scales', 'RMariaDB', 'glue', 'config', 'anytime', 'cli',
  'lifecycle', 'RSQLite', 'usethis', 'RPostgres'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'prettyunits', 'lubridate', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nortest', 'sjmisc', 'stringr', 'magrittr', 'crayon'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ggplot2', 'sjlabelled', 'ztable', '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:
  'dplyr', 'lubridate', 'tibble', 'readr', 'hms'
Note: found 13 marked UTF-8 strings
Package suggested but not available for checking: 'scatterplot3d'
mopsocd : initialize_pop: no visible global function definition for
  'runif'
mopsocd : compute_velocity: no visible global function definition for
  'runif'
mopsocd : mutate: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available: 'psych', 'gplots', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
checkTH: no visible global function definition for 'pchisq'
getOrderPval: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'party', 'partykit', 'varImp', 'plyr', 'foreach', 'measures', 'iml',
  'pdp', 'vip', 'ggplot2', 'rlang'

Packages suggested but not available for checking:
  'doParallel', 'knitr', 'rmarkdown', 'rmdformats', 'GDAtools',
  'RColorBrewer', 'caret', 'pROC', 'tidyverse', 'e1071'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
ametrine : <anonymous>: no visible global function definition for
  'approx'
ametrine: no visible global function definition for 'rgb'
isolum : <anonymous>: no visible global function definition for
  'approx'
isolum: no visible global function definition for 'rgb'
morgenstemning : <anonymous>: no visible global function definition for
  'approx'
morgenstemning: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
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', 'magrittr', 'morphemepiece.data', 'piecemaker', 'purrr',
  'readr', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'dplyr', 'fs', 'ggplot2', 'here', 'knitr', 'remotes', 'rmarkdown',
  'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'jointDiag', 'pracma'

Packages suggested but not available for checking:
  'devtools', 'flexmix', 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Arothron', 'Rvcg', 'Morpho', 'oce', 'rgdal', 'raster', 'sp',
  'geometry', 'rgl', 'colorRamps', 'DescTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rvcg', 'rgl', 'foreach', 'doParallel', 'colorRamps', 'Rcpp',
  'jsonlite', 'bezier', 'RcppArmadillo'

Packages suggested but not available for checking:
  'car', 'shapes', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'candisc', 'car', 'ellipse', 'heplots', 'plot3D',
  'StatMatch', 'vegan'

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: 'rgl', 'reshape2', 'igraph', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
cor.gen: no visible global function definition for 'rnorm'
cor.gen: no visible global function definition for 'resid'
cor.gen: no visible global function definition for 'lm'
cor.gen: no visible binding for global variable 'sd'
cor.gen: no visible global function definition for 'cor'
cor.gen: no visible global function definition for 'write.table'
stat.gen: no visible global function definition for 'rexp'
stat.gen: no visible global function definition for 'rnorm'
stat.gen: no visible binding for global variable 'sd'
stat.gen: no visible global function definition for 'write.table'
Undefined global functions or variables:
  cor lm resid rexp rnorm sd write.table
Consider adding
  importFrom("stats", "cor", "lm", "resid", "rexp", "rnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages required but not available:
  'coda', 'deSolve', 'dplyr', 'epitools', 'ggplot2', 'gridExtra',
  'magrittr', 'reshape2', 'rjags', 'tibble', 'tidyr', 'zoo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'Rdpack', 'reshape2', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tidyr', 'dplyr', 'ggplot2',
  'RCurl'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'crch', 'pbapply'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'minpack.lm', 'RCurl', 'pbapply', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'scales', 'pracma'

Packages suggested but not available for checking:
  'knitr', 'tidyverse', 'rmarkdown', 'reshape2'

Packages which this enhances but not available for checking:
  'MortalityLaws', 'lifecontingencies'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'wpp2017'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mosaicCore', 'mosaic', 'ggformula', 'magrittr', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'mosaicData'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rlang', 'tidyr'

Packages suggested but not available for checking:
  'mosaicData', 'mosaic', 'ggformula', 'NHANES', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'mosaic', 'reshape2', 'ggplot2', 'dplyr', 'tidyr', 'ggformula'
Note: found 7 marked UTF-8 strings
Running examples in 'mosaicData-Ex.R' failed
The error most likely occurred in:

> ### Name: HeatX
> ### Title: Data from a heat exchanger laboratory
> ### Aliases: HeatX
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # We can test for heat exchange with the environment by checking to see if the 
> # heat gained by the cold water matches the heat lost by the hot water.
> C_p <- 4.182 / 60  # / 60 because measuring m in L/min
> HeatX2 <- 
+   dplyr::mutate(HeatX,
+     Q.cold = m.cold * C_p * (T.cold.out - T.cold.in),
+     Q.hot  = m.hot * C_p * (T.hot.out- T.hot.in),
+     Q.env  = Q.cold + Q.hot
+   )
Error in loadNamespace(x) : there is no package called 'dplyr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'mosaicCore', 'dplyr', 'caret', 'ggplot2', 'ggformula', 'lazyeval',
  'knitr', 'testthat', 'tibble', 'tidyr', 'tidyverse'

Packages suggested but not available for checking:
  'mosaic', 'mosaicData', 'randomForest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggformula', 'mosaicData', 'mosaicCore', 'ggplot2',
  'ggstance', 'ggridges', 'ggrepel', 'rlang', 'tidyr', 'readr',
  'latticeExtra', 'ggdendro', 'gridExtra', 'glue', 'broom', 'leaflet'

Packages suggested but not available for checking:
  'vdiffr', 'lubridate', 'magrittr', 'NHANES', 'RCurl', 'sp',
  'maptools', 'vcd', 'testthat', 'knitr', 'mapproj', 'rgl',
  'rmarkdown', 'covr', 'formatR', 'palmerpenguins'

Package which this enhances but not available for checking: 'manipulate'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/MinimalRgg.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ecr', 'BBmisc', 'checkmate', 'ParamHelpers', 'smoof', 'mlrCPO',
  'mlr', 'parallelMap'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'magrittr', 'testthat', 'praznik', 'mlrMBO',
  'emoa', 'DiceKriging', 'rgenoud', 'randomForest', 'digest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'assertthat', 'pracma', 'NlcOptim', 'nloptr', 'sfsmisc'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dbscan', 'Rtsne'

Packages suggested but not available for checking:
  'annotate', 'bigparallelr', 'bigstatsr', 'future.apply',
  'scatterpie', 'clValid', 'ComplexHeatmap', 'fpc', 'ggplot2',
  'ggpmisc', 'ggthemes', 'gridExtra', 'irlba', 'knitr', 'rmarkdown',
  'testthat', 'viridis', 'spelling', 'VennDiagram'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'RColorBrewer', 'plot3D', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quadprog', 'lpSolve', 'bnlearn', 'ggm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MBESS', 'ez', 'reshape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'LICORS', 'RSpectra'

Packages suggested but not available for checking:
  'covr', 'knitr', 'mclust', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'comat', 'philentropy', 'Rcpp', 'sf', 'stars', 'tibble',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'spdep', 'knitr', 'rmarkdown', 'testthat', 'terra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggraph', 'igraph', 'intergraph', 'network',
  'purrr', 'RColorBrewer', 'reshape2', 'reticulate', 'rlang', 'scales',
  'tibble', 'tidygraph'

Packages suggested but not available for checking:
  'ergm', 'knitr', 'pkgdown', 'rmarkdown', 'shiny', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'Rcpp', 'coda', 'ks', 'mvtnorm', 'caper'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'formatR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dygraphs'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Formula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'latticeExtra', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'pracma'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pracma', 'dplyr', 'tidyr', 'magrittr', 'ggplot2', 'scales', 'psych',
  'Rcpp', 'diptest', 'RColorBrewer', 'cstab', 'fastcluster', 'fields',
  'rlang', 'lifecycle'

Packages suggested but not available for checking: 'readbulk', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'chron', 'gdistance', 'elevatr', 'maptools', 'raster', 'rgdal',
  'rgeos', 'sp', 'spatstat.geom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CircStats', 'Rcpp', 'sp', 'geosphere', 'ggplot2', 'ggmap',
  'numDeriv', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/moveHMM-custom-plots.Rnw'
   'inst/doc/moveHMM-guide.Rnw'
   'inst/doc/moveHMM-starting-values.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geosphere', 'sp', 'raster', 'rgdal', 'httr', 'memoise', 'xml2',
  'Rcpp'

Packages suggested but not available for checking:
  'adehabitatHR', 'adehabitatLT', 'markdown', 'rmarkdown', 'circular',
  'ggmap', 'mapproj', 'maptools', 'testthat', 'knitr', 'ggplot2',
  'leaflet', 'lubridate', 'ctmm', 'amt', 'bcpa', 'EMbC'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'move', 'raster', 'sf', 'lwgeom', 'slippymath', 'lubridate', 'curl',
  'ggplot2', 'cowplot', 'magick', 'gifski', 'av', 'pbapply', 'magrittr'

Packages suggested but not available for checking:
  'mapview', 'leaflet', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'move', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'skmeans', 'clue', 'slam'

Packages suggested but not available for checking:
  'tm', 'vcd', 'SnowballC', 'HSAUR3', 'colorspace',
  'corpus.useR.2008.abstracts', 'flexmix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'R.utils', 'changepoint', 'glmnet', 'HDPenReg', 'spikeslab'

Packages suggested but not available for checking:
  'CGHcall', 'aroma.affymetrix', 'aroma.cn', 'aroma.core',
  'aroma.light', 'snowfall', 'R.devices', 'R.filesets', 'R.methodsS3',
  'R.oo', 'matrixStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'pamr', 'pscl', 'numDeriv', 'foreach', 'doParallel', 'bst',
  'WeightSVM'

Packages suggested but not available for checking:
  'zic', 'R.rsp', 'knitr', 'rmarkdown', 'gdata', 'e1071', 'SparseM',
  'slam'

VignetteBuilder packages required for checking but not installed:
  'R.rsp', 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/brcancer.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlbench', 'bayesm', 'cvTools', 'mlogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'BH'

Packages suggested but not available for checking:
  'knitr', 'pinp', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'ggpubr', 'generics', 'tibble', 'dplyr', 'rlang',
  'stringr', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'spelling', 'covr', 'markdown',
  'tidyverse', 'modelsummary', 'broom'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lpSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'lme4'
Package required but not available: 'mvtnorm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'BiasedUrn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running examples in 'MPkn-Ex.R' failed
The error most likely occurred in:

> ### Name: MPkn-package
> ### Title: Calculations of One Discrete Model in Several Time Steps
> ### Aliases: MPkn-package
> 
> ### ** Examples
> 
> require(MPkn)
> require(markovchain)
Loading required package: markovchain
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'markovchain'
> options(digits = 14)
> n = 12
> k = 2
> rz = 11
> P = array(0, c(rz, rz))
> for (i in 1:rz){
+   po = runif(rz)
+   P[i, ] = po/sum(po)
+ }
> I = diag(1, rz, rz)
> Myy = MUPkL(P, P, I, n, k, c(1:rz))
> StSy = NULL
> for (i in 1:rz) StSy = c(StSy, Myy$Navg[,,i][n])
> mrkv = new("markovchain", transitionMatrix = P)
Error in getClass(Class, where = topenv(parent.frame())) : 
  "markovchain" is not a defined class
Calls: new -> getClass
Execution halted
Packages required but not available:
  'leaps', 'foreach', 'bestglm', 'doParallel', 'doRNG', 'plyr',
  'shinydashboard', 'shiny', 'glmnet', 'googleVis', 'ggplot2',
  'reshape2', 'scales', 'dplyr', 'tidyr', 'magrittr'

Packages suggested but not available for checking:
  'knitr', 'mvoutlier', 'glmulti', 'rmarkdown', 'DT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'gsubfn', 'coda', 'xtable', 'texreg', 'pander', 'digest',
  'ggplot2', 'data.table', 'rlang', 'fastDummies', 'checkmate'

Packages suggested but not available for checking:
  'rhdf5', 'relimp', '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: 'MplusAutomation', 'rpart.plot'

Package suggested but not available for checking: 'lavaan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/r_packages/pkgcheck/CRAN/mpmi/mpmi.Rcheck/00install.out' for details.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'KernSmooth' 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  'packageDescription'
export.summary.mpm: no visible global function definition for
  'write.table'
mpm: no visible binding for global variable 'median'
plot.mpm: no visible global function definition for 'rainbow'
plot.mpm: no visible global function definition for 'quantile'
plot.mpm: no visible global function definition for 'par'
plot.mpm: no visible global function definition for 'points'
plot.mpm: no visible global function definition for 'smoothScatter'
plot.mpm: no visible global function definition for 'colorRampPalette'
plot.mpm: no visible global function definition for 'symbols'
plot.mpm: no visible global function definition for 'text'
plot.mpm: no visible global function definition for 'lines'
plot.mpm: no visible global function definition for 'box'
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'stringr', 'stringi', 'partitions', 'plyr', 'ggplot2', 'polynom',
  'orthopolynom', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'magrittr', 'dplyr', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
place: no visible global function definition for 'points'
plot,mproc: no visible binding for global variable 'rainbow'
plot,mproc: no visible global function definition for 'plot.default'
plot,mproc: no visible global function definition for 'axis'
plot,mproc: no visible global function definition for 'points'
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'qtl', 'igraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qtl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ape'

Packages suggested but not available for checking:
  'knitr', 'caper', 'xtable'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/PEM_with_MPSEM.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'numDeriv', 'Brobdingnag', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking: 'snowfall', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/mptinr_introduction.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'tidyr', 'dplyr', 'tibble', 'rlang', 'reshape2',
  'ggplot2', 'MPTinR', 'TreeBUGS', 'runjags', 'coda', 'purrr', 'readr',
  'limSolve'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'sp', 'animation', 'zoo', 'rasterVis', 'latticeExtra',
  'viridis'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rgdal', 'devtools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pch', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'qtl', 'outliers'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'mvtnorm', 'multcomp', 'survPresmooth'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'plyr', 'BH', 'RcppEigen',
  'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'rjags', 'tidyverse', 'knitr', 'ggplot2', 'ggmcmc',
  'DescTools', 'bayesmeta', 'kableExtra', 'roxygen2', 'bookdown',
  'MendelianRandomization'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'maps', 'fields', 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'glasso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tables'

Package suggested but not available for checking: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'optimx', 'numDeriv', 'Rsolnp'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'xml2', 'wellknown', 'rappdirs', 'sp',
  'data.table', 'tibble'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'geojsonio', 'rgdal', 'rgeos', 'knitr',
  'rmapshaper'

Package which this enhances but not available for checking: 'leaflet'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
densityfn: no visible global function definition for 'dnbinom'
densityfn: no visible global function definition for 'dpois'
densityfn: no visible global function definition for 'dgeom'
form.add: no visible global function definition for 'formula'
mreg: no visible global function definition for 'model.frame'
mreg: no visible global function definition for 'model.response'
mreg: no visible global function definition for 'model.matrix'
mreg: no visible global function definition for 'model.offset'
mreg: no visible global function definition for 'nlm'
paper: no visible global function definition for 'model.matrix'
randfn: no visible global function definition for 'rnbinom'
randfn: no visible global function definition for 'rpois'
randfn: no visible global function definition for 'rgeom'
randfn: no visible global function definition for 'rbinom'
summary.mreg: no visible global function definition for 'pnorm'
summary.mreg: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  dgeom dnbinom dpois formula model.frame model.matrix model.offset
  model.response nlm pnorm printCoefmat rbinom rgeom rnbinom rpois
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dpois", "formula",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "nlm", "pnorm", "printCoefmat", "rbinom",
             "rgeom", "rnbinom", "rpois")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'dplyr', 'tidyr', 'ggplot2', 'Rdpack', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'glue'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'glmnet', 'grplasso', 'plyr', 'randtoolbox', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'purrr', 'plyr', 'ggplot2', 'dplyr', 'caret', 'gridExtra',
  'magrittr', 'reshape2', 'sfsmisc', 'igraph', 'pbapply'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'abind', 'geometry', 'matrixStats', 'reshape2',
  'RcppEigen', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'limSolve', 'DEoptim', 'forecast', 'monmlp', 'nnfor'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mrgsolve', 'dplyr', 'future', 'future.apply', 'callr', 'fst'

Packages suggested but not available for checking:
  'testthat', 'arrow', 'qs', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mrgsolve', 'withr', 'purrr', 'dplyr', 'assertthat', 'rlang',
  'ggplot2', 'tidyselect', 'tidyr', 'tibble', 'patchwork'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'magrittr', 'tibble', 'rlang', 'tidyselect',
  'lifecycle', 'glue', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'testthat', 'xml2', 'rmarkdown', 'yaml', 'knitr', 'data.table',
  'pmxTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'IHSEP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'KMsurv', 'coda'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'misc3d', 'oro.nifti'

Package suggested but not available for checking: 'tkrplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'lars', 'Rcpp', 'foreach', 'ncvreg', 'coin', 'shinyjs',
  'data.table', 'doParallel', 'sampling', 'bigmemory', 'mrMLM', 'sbl',
  'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lars', 'Rcpp', 'foreach', 'ncvreg', 'coin', 'sampling',
  'data.table', 'doParallel', 'sbl', 'BEDMatrix', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'matrixcalc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bnlearn', 'compositions', 'dynamicTreeCut', 'GGally', 'fastcluster',
  'gtools', 'graph', 'Hmisc', 'mice', 'network', 'pcalg', 'psych',
  'Rgraphviz', 'sna', 'WGCNA', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'R6', 'stringr', 'stringi', 'magrittr', 'assertthat',
  'base64enc', 'rvest', 'xml2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nortest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'igraph'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'data.table'

Package suggested but not available for checking: 'testthat'

Package which this enhances but not available for checking: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'yaml', 'magrittr', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'visNetwork', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'igraph', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magic'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rjags', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'ncvreg', 'foreach', 'mvtnorm'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'doParallel'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magic', 'abind'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magic', 'abind'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ade4', 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'htmlwidgets'

Packages suggested but not available for checking:
  'Biostrings', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'crayon', 'xml2', 'reshape2', 'ggplot2', 'ggfortify',
  'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Packages required but not available: 'Rcpp', 'RcppParallel'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'officer', 'cellranger', 'writexl', 'xml2', 'htmltools'

Package suggested but not available for checking: 'tinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'e1071', 'MALDIquant', 'MALDIrppa', 'MALDIquantForeign', 'mixOmics',
  'caret', 'reshape2', 'ggplot2', 'dplyr', 'fuzzyjoin', 'VSURF',
  'metap', 'xgboost', 'glmnet'

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:
  'lpSolve', 'ggplot2', 'lpSolveAPI', 'Rglpk', 'Rdpack'

Packages suggested but not available for checking:
  'Synth', 'DEoptim', 'rgenoud', 'DEoptimR', 'GenSA', 'GA', 'soma',
  'cmaes', 'Rmalschains', 'NMOF', 'nloptr', 'hydroPSO', 'pso',
  'LowRankQP', 'kernlab', 'reshape', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'phangorn', 'RandomFieldsUtils', 'zipfR', 'Rdpack', 'foreach',
  'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'Rdpack', 'kSamples'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'pander', 'stringi', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'mscsweblm4r'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'tuneR'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr', 'testthat', 'rvest', 'xml2', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'pander'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'mscstexta4r'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cv.msda: no visible global function definition for 'predict'
formatoutput: no visible global function definition for 'new'
msda.prep: no visible global function definition for 'cov'
plot.msda: no visible global function definition for 'par'
plot.msda: no visible global function definition for 'matplot'
plot.msda: no visible global function definition for 'rainbow'
plot.msda: no visible global function definition for 'approx'
plot.msda: no visible global function definition for 'axis'
predict.msda: no visible binding for global variable 'sd'
predict.msda: no visible global function definition for 'predict'
zeromat: no visible global function definition for 'new'
Undefined global functions or variables:
  approx axis cov matplot new par predict rainbow sd
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cov", "predict", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'sde', 'moments', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'whisker', 'RcppProgress'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'RcppProgress'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'snowfall', 'abind', 'dplyr', 'ggplot2', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'broom', 'covr', 'crayon', 'devtools', 'DT', 'fmsb', 'ggrepel',
  'gridExtra', 'kableExtra', 'knitr', 'mvtnorm', 'openxlsx', 'r4ss',
  'readxl', 'reshape2', 'rfishbase', 'rmarkdown', 'shiny', 'testthat',
  'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nnfor', 'MSGARCH', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'coda', 'zoo', 'expm', 'fanplot', 'numDeriv', 'RcppArmadillo'

Packages suggested but not available for checking: 'mcmc', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sglOptim', 'Rcpp', 'RcppProgress', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RColorBrewer'

Packages suggested but not available for checking:
  'animation', 'igraph', 'maps', 'mvtnorm', 'rgl', 'RgoogleMaps',
  'plotrix', 'ggplot2', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rlang', 'purrr'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'purrr', 'dplyr', 'forcats', 'stringr', 'ggplot2',
  'ggbeeswarm', 'rlang', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'insuranceData', 'reticulate', 'caret',
  '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:
  'babelgene', 'dplyr', 'magrittr', 'rlang', 'tibble', 'tidyselect'

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:
  'do', 'rvest', 'xml2', 'set', 'plyr', 'httr', 'jsonlite',
  'kableExtra', 'tmcn', 'crayon', 'dplyr', 'stringr', 'sqldf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doParallel', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'magrittr', 'plyr', 'PRROC', 'caret',
  'e1071', 'mice', 'pROC', 'ranger'

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.
Package required but not available: 'mclust'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rgl'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'changepoint', 'forecast', 'plyr', 'Rssa', 'tseries', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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: 'mvtnorm', 'expm'

Packages suggested but not available for checking:
  'mstate', 'minqa', 'doParallel', 'foreach', 'numDeriv', 'testthat',
  'flexsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'msm', 'ggplot2', 'patchwork', 'scales'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'roxygen2', 'usethis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mclust', 'tree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nleqslv', 'ggplot2', 'ggpubr', 'foreach', 'iterators', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gtools', 'reshape2', 'dplyr'

Packages suggested but not available for checking:
  'tidyverse', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'nloptr', 'RcppArmadillo', 'testthat'

Packages suggested but not available for checking: 'testthat', 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'dplyr', 'lubridate', 'magrittr', 'progress', 'purrr',
  'rlang', 'sjlabelled', 'stringr', 'tidyselect', 'tidytable', 'tidyr'

Packages suggested but not available for checking:
  'haven', 'tibble', 'rmarkdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RODBC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'graph'

Packages suggested but not available for checking: 'KMsurv', 'Rgraphviz'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'data.table', 'RColorBrewer', 'viridisLite'

Packages suggested but not available for checking:
  'cmprsk', 'ggplot2', 'knitr', 'rmarkdown', 'relsurv'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'knitr', 'rmarkdown'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'reshape2', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'expm', 'PP', 'mirt', 'scDIFtest', 'eRm'

Packages suggested but not available for checking:
  'mvtnorm', 'testthat', 'knitr', 'rmarkdown', 'strucchange'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'doParallel', 'latex2exp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'doParallel', 'nls2', 'RColorBrewer', 'plotrix'

Packages suggested but not available for checking:
  'RSQLite', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'partykit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'crul', 'openssl', 'jsonlite', 'data.table', 'R6',
  'rstudioapi', 'shinyjs', 'shiny'

Packages suggested but not available for checking:
  'httptest', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'entropy'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'sf'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ineq', 'png', 'mapsf'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CompQuadForm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'htmltools', 'ggplot2', 'scales', 'labeling'

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:
  'data.table', 'XML', 'stringr', 'plyr', 'dplyr', 'ggplot2',
  'magrittr', 'lubridate', 'tidyr', 'dtw', 'proxy'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'roxygen2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quantreg', 'glmnet', 'rqPen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'car'
'LazyData' is specified without a 'data' directory
Running examples in 'mthapower-Ex.R' failed
The error most likely occurred in:

> ### Name: mthapower
> ### Title: Power calculations - mtDNA haplogroups
> ### Aliases: mthapower
> 
> ### ** Examples
> 
> # Example 1:
> pow <- mthapower(n.cases=203, p0=0.443, Nh=13, OR.cas.ctrl=2.33, sig.level=0.05)
> 
> # Example 2:
> # Create data frames
> pow.H150 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.5, sig.level=0.05)
> pow.H175 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.75, sig.level=0.05)
> pow.H200 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2, sig.level=0.05)
> pow.H250 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2.5, sig.level=0.05)
> 
> # Bind the three data frames:
> bindata <- rbind(pow.H150,pow.H175,pow.H200,pow.H250)
> # Adds column OR to binded data frame:
> bindata$OR <- rep(factor(c(1.50,1.75,2,2.5)),
+               times = c(nrow(pow.H150),
+                         nrow(pow.H175),
+                         nrow(pow.H200),
+                         nrow(pow.H250)))
> # Create plot:
> # install.packages("car")
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
Packages required but not available:
  'stringr', 'XML', 'sensitivity', 'lhs', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'reshape2', 'testthat', 'vdiffr', 'covr', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'e1071'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'reshape2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'e1071', 'randomForest', 'pls', 'ellipse', 'latticeExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'png', 'jpeg', 'tiff', 'bmp', 'magick', 'imager', 'dplR',
  'spatstat.geom', 'measuRing', 'shiny', 'dplyr', 'shinydashboard',
  'shinyWidgets'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'shinytest', 'mockery', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'fGarch', 'fBasics', 'mvtnorm', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'epiDisplay', 'ggplot2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'capushe', 'shiny', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 2632 marked UTF-8 strings
Packages required but not available:
  'ggplot2', 'dplyr', 'jsonlite', 'tibble', 'magrittr', 'stringr',
  'readr', 'tidyr', 'lubridate', 'rlang', 'tidyselect', 'withr',
  'glue', 'fs'

Packages suggested but not available for checking:
  'testthat', 'sf', 'covr', 'hms', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'ggplot2', 'zoo', 'reshape2', 'broom', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'DiceKriging'

Package suggested but not available for checking: 'rgenoud'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deldir', 'splancs', 'sp', 'conf.design', 'Hmisc', 'dplyr', 'purrr',
  'gtools', 'magrittr', 'plyr', 'polyclip', 'rgeos', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'geozoo', 'plotly', 'kableExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DiagrammeR', 'dplyr', 'stringr'

Package suggested but not available for checking: 'htmlwidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RColorBrewer'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'rgl', 'randomcoloR', 'shape'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gtools', 'digest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rglpk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'scales', 'geometry', 'deldir', 'mirt', 'GPArotation', 'optimr',
  'Hmisc', 'car', 'dunn.test', 'gplots', 'polycor', 'dae', 'rgl',
  'xtable', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rmumps', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'TH.data', 'sandwich'

Packages suggested but not available for checking:
  'lme4', 'robustbase', 'coin', 'xtable', 'lmtest', 'coxme', 'SimComp',
  'ISwR', 'tram', 'fixest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'multcomp', 'pgirmess'
Running examples in 'multcompView-Ex.R' failed
The error most likely occurred in:

> ### Name: multcompBoxplot
> ### Title: boxplot with multcomp graphics
> ### Aliases: multcompBoxplot
> ### Keywords: aplot
> 
> ### ** Examples
> 
> 
> # Example from help("TukeyHSD")
> multcompBoxplot(breaks~tension, data=warpbreaks)
> # 'sortFn' can be either a function or a function name
> # default order is 'decreasing=TRUE'
> multcompBoxplot(breaks~tension, data=warpbreaks,
+        sortFn=median, decreasing=FALSE)
> 
> ##################
> library(multcomp)
Error in library(multcomp) : there is no package called 'multcomp'
Execution halted
Package required but not available: 'MTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'SimComp'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gnm', 'VGAM', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rticles'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'doParallel', 'foreach', 'plyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'zoo', 'pracma', 'wrapr', 'hablar', 'ggplot2'

Packages suggested but not available for checking:
  'readxl', 'readr', 'magic', 'Jmisc', 'functional', 'cowplot',
  'powerplus', 'reshape2', 'sjmisc', 'stringr', 'knitr', 'rmarkdown',
  'bookdown', 'kableExtra', 'neldermead', 'magrittr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
synthetic_multiband: no visible global function definition for 'runif'
synthetic_multiband: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available: 'Rcpp', 'RcppParallel', 'BH'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'MCMCpack', 'ggplot2',
  'matrixStats', 'plotrix'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/SIRtrans.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgl', 'tkrplot', 'tcltk2', 'shapes', 'dendroextras'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'car', 'FactoMineR', 'geigen', 'knitr', 'lme4', 'mixlm',
  'plotrix', 'pls', 'plsVarSel', 'pracma', 'progress', 'r.jive',
  'Rcpp', 'RegularizedSCA', 'RGCCA', 'RSpectra', 'SSBtools',
  'RcppEigen'

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:
  'Brobdingnag', 'coda', 'mvtnorm', 'purrr', 'Rcpp', 'magrittr',
  'progress', 'Rdpack', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bitops', 'multcomp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'igraph', 'plotly', 'shiny', 'shinythemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ranger', 'Boruta', 'dunn.test', 'caret', 'e1071', 'rdist'

Packages suggested but not available for checking:
  'BiocManager', 'Biobase', 'switchBox', 'knitr', 'rmarkdown',
  'BiocStyle', 'leukemiasEset', 'qpdf'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
calculate_direction: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Packages required but not available:
  'cowsay', 'crayon', 'dplyr', 'glue', 'magrittr', 'purrr', 'stringi',
  'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'fansi', 'knitr', 'rmarkdown', 'testthat', 'viridisLite',
  'wesanderson'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'psych', 'abind', 'foreach', 'mvtnorm', 'sciplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nbpMatching', 'crossmatch'

Package suggested but not available for checking: 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'lme4', 'pcaMethods', 'misc3d', 'RColorBrewer',
  'gridGraphics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'callr', 'crayon', 'dplyr', 'magrittr', 'qs', 'R6', 'rlang',
  'tibble', 'vctrs', 'tidyselect'

Packages suggested but not available for checking:
  'covr', 'knitr', 'lubridate', 'nycflights13', 'rmarkdown',
  'testthat', 'vroom', 'withr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'glmnet', 'pROC', 'lavaan', 'emmeans', 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'funData', 'MFPCA', 'sparseFLMM', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'ez', 'stringr', 'reshape2', 'tibble', 'ggplot2',
  'effsize', 'BayesFactor', 'bayestestR', 'broom', 'effectsize', 'esc',
  'forestplot', 'bootstrap'

Packages suggested but not available for checking:
  'gridExtra', 'fastDummies', 'vctrs', 'tidyselect', 'tidyr', 'plyr',
  'ggraph', 'igraph', 'testthat', 'cowplot', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'data.table', 'RcppArmadillo'

Packages suggested but not available for checking:
  'png', 'qgraph', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'mvtnorm', 'fastGHQuad'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'multiplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rmarkdown', '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:
  'mvtnorm', 'rlist', 'expm', 'ggplot2', 'gridExtra', 'cowplot',
  'plsgenomics', 'gplots', 'ggrepel', 'qgraph', 'mgm'

Packages suggested but not available 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'
Package required but not available: 'matlab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'limSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'parsnip', 'dplyr', 'lme4', 'purrr', 'rlang', 'tibble', 'withr'

Packages suggested but not available for checking:
  'contrast', 'covr', 'gee', 'knitr', 'rmarkdown', 'spelling',
  'testthat', 'tidymodels'

VignetteBuilder 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', 'xtable', 'PSAgraphics', 'plyr', 'psych', 'reshape',
  'party'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'lmerTest', 'data.table', 'extraoperators', 'JWileymisc',
  'cowplot', 'ggplot2', 'lavaan', 'zoo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sys', 'rappdirs', 'usethis', 'askpass'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'truncnorm', 'ordinalNet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'statmod', 'RMark', 'Brobdingnag', 'mvtnorm', 'prodlim',
  'sp', 'raster'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'diptest', 'ks', 'rootSolve'

Package suggested but not available for checking: 'nor1mix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'dplyr', 'lubridate', 'magrittr', 'stringr', 'rlang',
  'tidyselect', 'tidyr', 'devtools', 'sqldf'

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.
multinb.fit: no visible global function definition for 'nlminb'
multinbmod: no visible global function definition for 'is.empty.model'
multinbmod: no visible global function definition for 'model.matrix'
multinbmod: no visible binding for global variable 'contrasts'
multinbmod: no visible global function definition for 'model.response'
multinbmod: no visible global function definition for 'model.offset'
Undefined global functions or variables:
  contrasts is.empty.model model.matrix model.offset model.response
  nlminb
Consider adding
  importFrom("stats", "contrasts", "is.empty.model", "model.matrix",
             "model.offset", "model.response", "nlminb")
to your NAMESPACE file.
Packages required but not available: 'igraph', 'Rcpp', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'Rcpp'

Packages suggested but not available for checking:
  'sand', 'statnet', 'data.table', 'testthat', 'igraphdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'Rdpack', 'tibble',
  'dplyr', 'rlang', 'purrr', 'forcats', 'glue', 'randtoolbox',
  'copula', 'tidyr', 'stringr', 'igraph', 'ggraph', 'ggplot2',
  'ggdist', 'truncdist', 'bayesplot', 'BH', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'withr', 'knitr', 'rmarkdown', 'R.rsp', 'rprojroot',
  'loo', 'logitnorm', 'crayon', 'tidygraph', 'pkgdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'Rglpk', 'quadprog', 'coda', 'RcppXPtrUtils',
  'RcppArmadillo', 'RcppProgress'

Packages suggested but not available for checking:
  'rPorta', 'knitr', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgenoud', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gsl', '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.
Packages required but not available: 'mvtnorm', 'corpcor', 'psych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertive.base', 'assertive.files', 'assertive.numbers',
  'assertive.properties', 'assertive.types', 'ggplot2', 'gridGraphics',
  'gtable', 'magick', 'magrittr', 'stringi'

Packages suggested but not available for checking:
  'ComplexHeatmap', 'roxygen2', 'VennDiagram', 'knitr', 'rmarkdown',
  'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'epitools', 'meta', 'HardyWeinberg', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lars', 'penalized', 'polspline'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crayon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'patchwork', 'viridis'

Packages suggested but not available for checking: 'testthat', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'multigraph', 'Rgraphviz', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/TwoModeNetworks.Rnw'
(Is a VignetteBuilder field missing?)
Package unavailable to check Rd xrefs: 'multigraph'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/TwoModeNetworks.Rnw'
(Is a VignetteBuilder field missing?)
Package required but not available: 'lpSolveAPI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'abind'

Package suggested but not available for checking: 'polynom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'qpdf'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'pROC', 'risksetROC', 'snowfall'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'SuppDists', 'quantreg'
Package unavailable to check Rd xrefs: 'quantreg'
Running examples in 'MultiRobust-Ex.R' failed
The error most likely occurred in:

> ### Name: MR.quantile
> ### Title: Multiply Robust Estimation of the Marginal Quantile
> ### Aliases: MR.quantile
> 
> ### ** Examples
> 
> # Simulated data set
> set.seed(123)
> n <- 400
> gamma0 <- c(1, 2, 3)
> alpha0 <- c(-0.8, -0.5, 0.3)
> X <- runif(n, min = -2.5, max = 2.5)
> p.mis <- 1 / (1 + exp(alpha0[1] + alpha0[2] * X + alpha0[3] * X ^ 2))
> R <- rbinom(n, size = 1, prob = 1 - p.mis)
> a.x <- gamma0[1] + gamma0[2] * X + gamma0[3] * exp(X)
> Y <- rnorm(n, a.x, sd = sqrt(4 * X ^ 2 + 2))
> dat <- data.frame(X, Y)
> dat[R == 0, 2] <- NA
> 
> # Define the outcome regression models and missingness probability models
> imp1 <- glm.work(formula = Y ~ X + exp(X), family = gaussian)
> imp2 <- glm.work(formula = Y ~ X + I(X ^ 2), family = gaussian)
> mis1 <- glm.work(formula = R ~ X + I(X ^ 2), family = binomial(link = logit))
> mis2 <- glm.work(formula = R ~ X + exp(X), family = binomial(link = cloglog))
> MR.quantile(response = Y, tau = 0.25, imp.model = list(imp1, imp2),
+             mis.model = list(mis1, mis2), L = 10, data = dat)
Error in MR.quantile(response = Y, tau = 0.25, imp.model = list(imp1,  : 
  need CRAN package 'quantreg' for quantile estimation
Execution halted
Packages required but not available: 'zoo', 'magrittr'

Packages suggested but not available for checking: 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sensitivity', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/multisensi-vignette.rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AROC', 'coxme', 'lme4', 'lmerTest', 'logistf', 'metafor', 'pROC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'statmod', 'psych', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MaxSkew'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'kohonen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CCM_boot : <anonymous>: no visible global function definition for 'sd'
SSR_check_signal: no visible global function definition for 'cor'
SSR_check_signal: no visible global function definition for 'cor.test'
SSR_check_signal: no visible global function definition for 'lm'
SSR_pred_boot: no visible global function definition for 'cor'
make_ccm_data: no visible global function definition for 'rnorm'
make_ccm_data: no visible global function definition for 'runif'
make_ccm_data: no visible global function definition for 'rlnorm'
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
Packages required but not available:
  'clValid', 'clv', 'dplyr', 'foreach', 'ggplot2', 'igraph', 'ltm',
  'plyr', 'poweRlaw', 'reshape2', 'RColorBrewer', 'rlang', 'rmutil'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'mclust', 'testthat', 'gridExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'reshape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'psd', 'astrochron', 'fftwtools', 'slp'
Package required but not available: 'gplots'

Package suggested but not available for checking: 'CCA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'Rcpp', 'microbenchmark'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'PCAmixdata', 'candisc', 'biotools', 'corrplot', 'crayon', 'ape'

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', 'bootstrap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BinOrdNonNor', 'CorrToolBox', 'corpcor', 'moments', 'norm',
  'PoisNonNor'

Package suggested but not available for checking: 'PoisBinOrdNonNor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'vars', 'reshape2', 'RcppArmadillo'

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.
Package required but not available: 'glmnet'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'emulator', 'mvtnorm', 'mathjaxr'

Package suggested but not available for checking: 'abind'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'dplyr', 'purrr', 'rlang', 'R6', 'tidyr', 'tibble',
  'magrittr', 'tidyselect', 'formatR', 'collections', 'evaluate',
  'rstudioapi', 'berryFunctions'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'highr', 'lubridate', 'rmarkdown', 'covr',
  'broom', 'gganimate', 'gifski', 'forcats', 'stringr', 'cowplot',
  'tidybayes', 'png', 'stringi', 'modelr', 'styler'

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', 'waldo', 'devtools', 'withr', 'callr'
Running 'testthat.R'
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:
  'mclust', 'matrixStats', 'randnet', 'irlba', 'doParallel', 'foreach'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CMLS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sandwich'

Package suggested but not available for checking: 'lmtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ICSNP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'statmod', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'Rdpack', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MultivariateRandomForest'

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', 'pdist', 'pls', 'gplots', 'mvtnorm', 'robustbase', 'gtools',
  'bitops', 'caTools', 'pcaPP', 'rrcov'

Depends: includes the non-default packages:
  'car', 'pdist', 'pls', 'gplots', 'mvtnorm', 'robustbase', 'gtools',
  'bitops', 'caTools', 'pcaPP', 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'lme4', 'gamm4', 'geepack'

Packages which this enhances but not available for checking:
  'aod', 'aods3', 'betareg', 'caper', 'coxme', 'cplm', 'gee', 'glmmML',
  'logistf', 'MCMCglmm', 'ordinal', 'pscl', 'spdep', 'spatialreg',
  'splm', 'unmarked', 'geeM', 'gamlss'
Packages unavailable to check Rd xrefs: 'AICcmodavg', 'bbmle', 'glmulti', 'arm', 'performance', 'gee', 'geepack', 'geeM', 'wgeesel', 'ape', 'bestglm', 'leaps', 'lme4', 'cplm', 'gamm4', 'gamlss', 'glmmML', 'glmmTMB', 'MCMCglmm', 'pscl', 'aod', 'aods3', 'betareg', 'brglm', 'spatialreg', 'splm', 'coxme', 'quantreg', 'ordinal', 'logistf', 'caper', 'maxlike', 'RMark'
Packages required but not available:
  'lme4', 'TMB', 'Rcpp', 'stringr', 'RcppEigen'

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'memisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rootSolve', 'spacesRGB', 'spacesXYZ'

Packages suggested but not available for checking:
  'microbenchmark', 'knitr', 'rmarkdown', 'flextable'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/lightness.rnw'
   'inst/doc/lociHC.rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'colorspace'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'maps', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'clue', 'lpSolve'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FNN', 'ggplot2', 'gridExtra', 'gtools', 'plyr', 'proxy', 'reshape2',
  'signal', 'umap'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'magrittr', 'qmap', 'lubridate'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'seewave'

Package suggested but not available for checking: 'plsgenomics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'audio', 'crayon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'DescTools', 'pander'
Packages required but not available:
  'digest', 'formatR', 'qs', 'tibble', 'here'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling', 'testthat', 'tictoc'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
prentice.test: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available:
  'mutoss', 'multcomp', 'plotrix', 'rJava', 'JavaGD', 'CommonJavaJars',
  'JGR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'plotrix', 'multtest', 'multcomp'

Packages suggested but not available for checking:
  'fdrtool', 'qvalue', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Familias', 'paramlink', 'expm', 'IBDsim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'doParallel', 'ggplot2', 'pracma', 'proxy'

Packages suggested but not available for checking:
  'dplyr', 'reshape2', 'kableExtra', 'gridExtra', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'runner'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sm', 'gtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'tweedie', 'statmod', 'RcppGSL'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'HSAUR2'

Packages suggested but not available for checking:
  'mvtnorm', 'mclust', 'flexclust', 'RLRsim', 'multcomp', 'ape', 'sem',
  'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rattle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Formula', 'MNM', 'quantreg', 'Rfit', 'SpatialNP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'dummies', 'ggplot2', 'moments', 'penalized', 'plyr',
  'reshape2', 'sn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'WeightIt', 'cobalt', 'matrixNormal', 'geometry', 'sp',
  'gbm', 'CBPS'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'dagitty', 'ggdag', 'dplyr', 'rmarkdown',
  '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: 'car', 'heplots'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Package required but not available: 'CompQuadForm'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fields', 'wavethresh', 'xts', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rcdd', 'rgl', 'geometry', 'abind', 'SimplicialCubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mixmeta'

Packages suggested but not available for checking:
  'metafor', 'meta', 'rmeta', 'dlnm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BMS', 'dplyr', 'lazyeval', 'plyr', 'rlang', 'xts', 'zoo',
  'robustbase'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'phytools', 'ape', 'corpcor', 'subplex', 'spam', 'glassoFast',
  'pbmcapply'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'car'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'plyr'

Packages suggested but not available for checking: 'rgl', 'Rfast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'mvtnorm', 'microbenchmark',
  'plyr', 'RhpcBLASctl'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'nortest', 'moments', 'copula'

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
mvnpermute: no visible global function definition for 'lm'
mvnpermute: no visible global function definition for 'coef'
mvnpermute: no visible global function definition for 'resid'
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
Packages required but not available:
  'nortest', 'moments', 'plyr', 'psych', 'energy', 'car'

Packages suggested but not available for checking:
  'BiocStyle', 'knitr', 'rmarkdown'

VignetteBuilder 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', 'knitr', 'ggplot2'

Package suggested but not available for checking: 'markdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'markdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'minqa', 'BB', 'ucminf', 'dfoptim', 'pbivnorm', 'optimx', 'mnormt',
  'numDeriv'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'xtable', 'colorspace'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sgeostat', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'invgamma'

Package suggested but not available for checking: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'evd', 'numbers', 'gmp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'Rcpp', 'partitions', 'mpoly', 'magic', 'digest',
  'disordR'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'microbenchmark', 'testthat', 'spray'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'maxLik', 'abind', 'bayesm', 'miscTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
mvorpb: no visible global function definition for 'pnorm'
mvorpb: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
Packages required but not available: 'data.table', 'statmod'

Packages suggested but not available for checking:
  'knitr', 'rgl', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotrix'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppThread'

Packages suggested but not available for checking:
  'dplyr', 'furrr', 'knitr', 'rmarkdown', 'stringr', 'testthat',
  'textmineR', 'tidytext', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
rtn: no visible global function definition for 'runif'
rtn: no visible global function definition for 'qnorm'
rtn: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Packages required but not available:
  'abind', 'ape', 'mvtnorm', 'ouch', 'PCMBase', 'TreeSim', 'matrixcalc'

Packages suggested but not available for checking:
  'PCMBaseCpp', 'geiger', 'ggplot2', 'knitr', 'rmarkdown', 'mvMORPH'

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: 'rrcov', 'mvtnorm', 'robustbase'

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: 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'mathjaxr', 'testthat', 'BioNet', 'roxygen2',
  'DLBCL'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'penalized'
Running examples in 'MWLasso-Ex.R' failed
The error most likely occurred in:

> ### Name: MWLasso
> ### Title: Penalized Moving-Window Lasso Method for Genome-Wide Association
> ###   Studies
> ### Aliases: MWLasso MW_parameters
> ### Keywords: model fitting
> 
> ### ** Examples
> 
> # In example 1, feature matrix X and response variable Y are randomly generated.
> # Example 1:
> n = 100
> p = 200
> X = matrix(rnorm(n*p, mean = 0, sd = 1), nrow = n, ncol = p)
> X[2,1] = NA; X[80:90,1]= NA; 
> Y =  rnorm(n, mean = 0, sd = 1)
> 
> number = 20
> gamma2 = 0.1
> d = 4
> params = MW_parameters(X, Y, d, number, gamma2, method="linear")
Tuning parameters are: lambda = 0.1413146, eta = 1.271831.> lambda = params[1]
> eta = params[2]
> beta.hat = MWLasso(X, Y, lambda, eta, d, method="linear")
> 
> # In example 2, the nki70 dataset is from the "penalized" package
> # (https://cran.r-project.org/web/packages/penalized/penalized.pdf).
> # The response variable Y is "event", the disease indicator.
> # The feature matrix X is "TSPYL5...C20orf46", the gene expression
> # measurements of 70 prognostic genes.
> # Example 2:
> require("penalized")
Loading required package: penalized
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'penalized'
> data(nki70)
Warning in data(nki70) : data set 'nki70' not found
> data = nki70
Error: object 'nki70' not found
Execution halted
Package required but not available: 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'htmltools'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'visNetwork', 'htmlwidgets'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rTensor', 'nnTensor', 'ccTensor', 'ica', 'igraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'OpenMx'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'tidyverse'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ordinal', 'quantreg', 'lme4', 'foreach', 'doParallel', 'relations',
  'Rfast', 'visNetwork', 'energy', 'geepack', 'knitr', 'dplyr',
  'bigmemory', 'coxme', 'Rfast2', 'Hmisc'

Packages suggested but not available for checking: 'markdown', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'rlang', 'fda', 'data.table', 'reticulate',
  'caret', 'e1071', 'ggplot2', 'tidyr', 'uwot', 'lme4', 'stringr',
  'kSamples', 'psych', 'fossil', 'glue'

Packages suggested but not available for checking:
  'knitr', 'janitor', 'testthat', 'rmarkdown', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
abcpred_nmer: no visible global function definition for 'write.table'
algpred: no visible global function definition for 'read.table'
algpred: no visible global function definition for 'write.table'
allermatch: no visible global function definition for 'read.table'
allermatch: no visible global function definition for 'write.table'
bcepred_nmer: no visible global function definition for 'write.table'
bimas_nmer: no visible global function definition for 'write.table'
filter.firstlayer: no visible global function definition for
  'read.table'
filter.firstlayer: no visible global function definition for
  'write.table'
iedb_arb_mhci_nmer: no visible global function definition for
  'write.table'
iedb_arb_mhcii_nmer: no visible global function definition for
  'write.table'
iedb_consensus_mhci_nmer: no visible global function definition for
  'write.table'
iedb_consensus_mhcii_nmer: no visible global function definition for
  'write.table'
netmhcNN_nmer: no visible global function definition for 'write.table'
netmhcWT_nmer: no visible global function definition for 'write.table'
propred_nmer: no visible global function definition for 'write.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'lmtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'nortest', 'fitdistrplus', 'foreach', 'doParallel', 'dplyr',
  'RColorBrewer', 'taxize', 'reshape2', 'ggplot2', 'readr', 'tibble',
  'scales', 'gridExtra', 'edgeR', 'RcppArmadillo', 'cpp11'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rms', 'mclogit'

Package suggested but not available for checking: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvest', 'httr', 'jsonlite', 'tibble', 'dplyr', 'lubridate',
  'urltools'

Packages suggested but not available for checking: 'httptest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppSpdlog', 'RcppEigen'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'stringi'

Packages suggested but not available for checking:
  'devtools', 'httr', 'jsonlite', 'magrittr', 'testthat', 'ISOcodes',
  'xml2', 'rmarkdown', 'roxygen2', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppEigen', 'BH'

Packages suggested but not available for checking: 'testthat', 'RANN'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'crayon', 'dplyr', 'ggbeeswarm', 'ggforce', 'ggplot2',
  'ggrepel', 'knitr', 'magrittr', 'purrr', 'rlang', 'rmarkdown',
  'rstudioapi', 'scales', 'sessioninfo', 'shiny', 'shinyWidgets',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'covr', 'Biobase', 'GEOquery', 'limma'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr3', 'mlr3pipelines', 'paradox', 'mlr3learners', 'missForest',
  'missMDA', 'doParallel', 'testthat', 'Amelia', 'VIM', 'softImpute',
  'missRanger', 'mice', 'data.table', 'foreach', 'glmnet'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'magrittr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'MCMCglmm', 'asreml'
Package unavailable to check Rd xrefs: 'MCMCglmm'
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'magrittr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'naflex-Ex.R' failed
The error most likely occurred in:

> ### Name: na_omit_if
> ### Title: Conditionally omit missing values
> ### Aliases: na_omit_if
> 
> ### ** Examples
> 
> x <- c(1, 3, NA, NA, NA, 4, 2, NA, 4, 6)
> 
> sum(na_omit_if(x, prop = 0.45, n = 10, consec = 5))
[1] 20
> sum(na_omit_if(x, prop = 0.45))
[1] 20
> 
> require(magrittr)
Loading required package: magrittr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'magrittr'
> sum(x %>% na_omit_if(prop = 0.45))
Error in x %>% na_omit_if(prop = 0.45) : could not find 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:
  'RColorBrewer', 'lifecycle', 'magrittr', 'mapdata', 'maps', 'rgdal',
  'rlang'

Packages suggested but not available for checking:
  'covr', 'here', 'knitr', 'readxl', 'rmarkdown', 'sp', 'testthat',
  'usethis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/intro_naivebayes.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/intro_naivebayes.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available: 'grpreg', 'gmm', 'ncvreg', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'assertthat'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'covr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'data.table', 're2r', 'knitr', 'rmarkdown', 'rex',
  'dplyr', 'tidyr', 'rematch2'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'data.table'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'htmltools', 'qrcode', 'here', 'lubridate', 'webshot', 'bib2df',
  'dplyr', '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.
Package suggested but not available for checking: 'Biostrings'
Package unavailable to check Rd xrefs: 'Biostrings'
Malformed Description field: should contain one or more complete sentences.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'udpipe'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bWGR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'autothresholdr', 'BBmisc', 'checkmate', 'detrendr',
  'dplyr', 'filesstrings', 'ggplot2', 'glue', 'ijtiff', 'magrittr',
  'purrr', 'Rcpp', 'reshape2', 'rlang', 'stringr', 'viridis', 'withr'

Packages suggested but not available for checking:
  'abind', 'covr', 'gridExtra', 'knitr', 'matrixStats', 'pacman',
  'rmarkdown', 'spelling', 'testthat', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'tidyr', 'tibble', 'norm', 'magrittr',
  'visdat', 'rlang', 'forcats', 'viridis', 'glue', 'UpSetR'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'rpart.plot', 'covr', 'gridExtra',
  'wakefield', 'vdiffr', 'here', 'simputation', 'imputeTS', 'gdtools',
  'Hmisc', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'distrEx', 'rgl'

Packages suggested but not available for checking: 'DEoptim', 'mco'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'ccaPP', 'dplyr', 'epiR', 'magrittr', 'purrr', 'rlang'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bit64', 'RcppCCTZ', 'zoo', 'Rcpp', 'RcppDate'

Packages suggested but not available for checking:
  'tinytest', 'data.table', 'xts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lubridate'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'strucchange', 'tseries', 'Formula', 'gtools', 'car'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'progress', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'dplyr', 'png', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'lubridate', 'jsonlite', 'readr', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'purrr', 'ratelimitr', 'rmarkdown', 'spelling', '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:
  'Rdpack', 'rdist', 'stabledist', 'beepr'

Packages suggested but not available for checking:
  'ppclust', 'spatialClust', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gh', 'remotes', 'usethis', 'curl', 'withr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'mockery', 'rstudioapi', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgl', 'nat', 'nabor', 'dendroextras', 'plyr', 'spam'

Packages suggested but not available for checking:
  'spelling', 'bigmemory', 'ff', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'rgl', 'nabor', 'igraph', 'filehash', 'digest', 'nat.utils', 'plyr',
  'yaml'

Packages suggested but not available for checking:
  'Rvcg', 'testthat', 'httr', 'XML', 'knitr', 'rmarkdown', 'markdown',
  'alphashape3d', 'webshot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crul', 'jsonlite', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'vcr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'Rglpk', 'plyr', 'pps', 'sampling', 'ggplot2', 'rlang',
  'ramify', 'slam'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'testthat', 'DT', 'stringr',
  'covr', 'gurobi'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nat', 'rgl', 'digest', 'igraph', 'memoise', 'rappdirs'

Packages suggested but not available for checking:
  'spelling', 'git2r', 'nabor', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyWidgets', 'dplyr', 'stringr', 'sp', 'raster',
  'shinydashboard', 'leaflet', 'leaflet.extras', 'tidytext',
  'magrittr', 'vegan', 'fasterize', 'sf', 'htmltools', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'tm', 'rgeos', 'rgdal',
  'rnaturalearth', 'lwgeom', 'shinyLP', 'maptools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'glmnet'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'issue-1.R'
Running the tests in 'tests/issue-1.R' failed.
Complete output:
  > stopifnot(require(testthat))
  Loading required package: testthat
  Error: require(testthat) is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  Execution halted
Packages required but not available: 'knitr', 'tuneR'

Package suggested but not available for checking: 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'cli', 'dplyr', 'pillar', 'purrr', 'rlang', 'tidyselect', 'vctrs'

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: 'hypergeo', 'testthat'
Package unavailable to check Rd xrefs: 'CBPS'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'magrittr', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggplot2', 'plyr', 'rvest', 'stringr', 'xml2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gplots', 'gtools'

Packages suggested but not available for checking: 'BiocGenerics', 'DEXSeq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'PWEALL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'dplyr'
Packages required but not available:
  'Rcpp', 'magrittr', 'rrpack', 'glmnet', 'RcppParallel', 'mpath',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'PoiClaClu', 'sSeq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magicaxis', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'qvalue'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NB.estimator: no visible global function definition for 'optimize'
NB.estimator: no visible global function definition for 'uniroot'
NB.example.dataset: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  optimize uniroot write.table
Consider adding
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rlang', 'caret', 'lubridate', 'poisbinom', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'Hmisc', 'igraph', 'knitr', 'pheatmap', 'RColorBrewer',
  'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'scales', 'gtable', 'knitr', 'xtable', 'reshape2', 'dplyr', 'Cairo',
  'readr', 'lazyeval', 'PopED', 'magrittr', 'rlang', 'purrr', 'tibble',
  'rmarkdown', 'tidyr', 'ggplot2', 'gridExtra', 'bookdown'

Package suggested but not available for checking: 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gplots', 'quantreg', 'sfa', 'lpSolve', 'ggplot2', 'doParallel',
  'foreach', 'iterators', 'plotly'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rtf', 'NonCompart'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
ncbit : FUN: no visible global function definition for 'read.table'
ncbit : FUN: no visible global function definition for 'head'
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
Packages required but not available: 'ncdf4', 'PCICt', 'abind'

Packages suggested but not available for checking: 'proj4', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RNetCDF', 'ncmeta', 'sf', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'pkgdown', 'sp', 'geoknife',
  'ncdf4', 'jsonlite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ncdf4'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
d0: no visible global function definition for 'qnorm'
dncgamma: no visible global function definition for 'dpois'
indncgamma: no visible global function definition for 'pgamma'
indncgamma: no visible global function definition for 'dpois'
inxncgamma: no visible global function definition for 'qnorm'
inxncgamma: no visible global function definition for 'pgamma'
inxncgamma: no visible global function definition for 'dpois'
pncgamma: no visible global function definition for 'pgamma'
pncgamma: no visible global function definition for 'dpois'
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
Packages required but not available:
  'dplyr', 'rlang', 'RNetCDF', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'proftools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'rhoR', 'cli'

Packages suggested but not available for checking:
  'testthat', 'magrittr', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'copula', 'Deriv', 'stringr', 'stringi'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'downloader', 'ggplot2', 'jsonlite', 'RColorBrewer'

Packages suggested but not available for checking:
  'cowplot', 'dplyr', 'DT', 'ggplotify', 'maps', 'magick', 'shiny',
  'shinyBS', 'shinydashboard', 'shinycssloaders', 'remotes', 'plotly',
  'prettydoc', 'knitr', 'rmarkdown', 'reshape2', 'ggrepel',
  'shadowtext', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

Packages suggested but not available for checking:
  'testthat', 're2r', 'stringi', 'ggplot2', 'tidyr', 'cdata',
  'reshape2', 'knitr', 'markdown', 'R.utils'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'yaImpute', 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'copula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'glmnet', 'mvtnorm', 'fields', 'RcppEigen'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ashr', 'knitr', 'rmarkdown', 'tinytest'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'Rcpp', 'data.table', 'tibble'

Packages suggested but not available for checking: 'tinytest', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'network', 'networkDynamic', 'animation', 'sna', 'statnet.common',
  'jsonlite', 'base64'

Packages suggested but not available for checking:
  'tergm', 'tsna', 'testthat', 'knitr', 'htmlwidgets', 'scatterplot3d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rdpack', 'sandwich', 'nonnest2', 'CompQuadForm'

Packages suggested but not available for checking:
  'knitr', 'pscl', 'AER', 'lmtest', 'mlogit', 'modelsummary',
  'bookdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'heatmaply', 'ConsensusClusterPlus', 'ggplot2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'Rcpp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'viridis', 'fBasics', 'data.table', 'bayestestR', 'pROC', 'MBESS',
  'car', 'ez', 'Exact', 'BayesFactor', 'ggplot2', 'ggpubr', 'logspline'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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:
  'Rcpp', 'nloptr', 'Rfast', 'trust', '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:
  'rtweet', 'randomForest', 'stringr', 'SnowballC', 'SparseM', 'tau',
  'tm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'combinat'
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Running 'run_tests.R'
Running the tests in 'tests/run_tests.R' failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'msm', 'bit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'roxygen2'
Packages required but not available:
  'DescTools', 'lavaan', 'WRS2', 'ggplot2', 'nptest', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'RDStreeboot', 'igraph', 'RDS', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'mlbench'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'optimbase', 'optimsimplex'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'base64enc', 'jsonlite', 'RCurl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'ssh', 'sys', 'fs', 'R.utils'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'attempt', 'data.table', 'glue', 'httr', 'igraph', 'jsonlite',
  'magrittr', 'purrr', 'R6', 'rlang', 'rstudioapi', 'shiny', 'tibble',
  'tidyr', 'tidyselect'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'zoo', 'httr', 'lubridate', 'neonUtilities', 'magrittr',
  'rhdf5', 'R.utils', 'tidyselect', 'data.table', 'rlang', 'lifecycle'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DBI', 'duckdb', 'httr', 'progress', 'R.utils', 'thor', 'vroom',
  'zip'

Packages suggested but not available for checking:
  'tibble', 'jsonlite', 'testthat', 'covr', 'xml2', 'spelling',
  'rstudioapi', 'neonUtilities', 'rhdf5', 'curl', 'openssl', 'digest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'downloader', 'data.table', 'R.utils', 'tidyr',
  'stringr', 'pbapply', 'curl'

Packages suggested but not available for checking:
  'rhdf5', 'raster', 'sp', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'reshape2', 'jsonlite', 'httr', 'xml2', 'analogue',
  'leaflet', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'PairedData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'reticulate', 'this.path', 'rstudioapi', 'ggplot2', 'plotly',
  'htmlwidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rappdirs', 'dplyr', 'purrr', 'readr', 'dataone'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'dplyr', 'Rcpp', 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dgof', 'pROC'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'rlang', 'vctrs', 'tidyselect'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'graph', 'magrittr'

Packages suggested but not available for checking:
  'BiocStyle', 'ggplot2', 'igraph', '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:
  'igraph', 'infotheo', 'corpcor', 'huge', 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'gtools', 'stringr', 'igraph'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MCMCpack', 'Rcpp', 'coda', 'ggplot2', 'mvtnorm', 'RcppArmadillo',
  'RcppProgress'

Packages suggested but not available for checking:
  'testthat', 'igraph', 'magic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rD3plot', 'igraph', 'haven'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'lavaan', 'shiny', 'htmltools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'gdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'clue', 'expm', 'igraph', 'pdist', 'pracma',
  'vegan', 'magrittr', 'foreach', 'doParallel', 'optimx', 'GenSA',
  'rlang', 'ggfortify', 'ggplot2', 'ggraph', 'reshape2'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'Rdpack', 'pracma', 'expm', 'RcppArmadillo'

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:
  'Rcpp', 'sna', 'network', 'networkDynamic', 'MatchIt', 'SparseM',
  'igraph', 'viridisLite', 'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown', 'ape', 'RSiena'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'arrangements', 'doParallel', 'dplyr', 'igraph', 'ggplot2', 'ggraph',
  'magrittr', 'patchwork', 'picante', 'rlang', 'Rfast', 'tibble',
  'tidygraph', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BBmisc', 'mvtnorm', 'lhs', 'checkmate', 'ggplot2', 'igraph',
  'stringr'

Packages suggested but not available for checking: 'testthat', 'lpSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'AnnotationDbi', 'corpcor', 'data.table', 'dplyr', 'genefilter',
  'graph', 'graphite', 'glmnet', 'glassoFast', 'httr', 'igraph',
  'jsonlite', 'magrittr', 'msigdbr', 'org.Hs.eg.db', 'quadprog',
  'RCy3', 'reshape2', 'rlang', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'ndexr', 'rmarkdown'

VignetteBuilder 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', 'qtl', 'glasso', 'RBGL', 'huge', 'tmvtnorm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'LIM'
EnvInd: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'igraph', 'brainGraph', 'Rdpack'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'abind', 'CircStats', 'data.table', 'matrixStats',
  'quickPlot', 'sp', 'SpaDES.tools', 'rgeos'

Packages suggested but not available for checking:
  'fastshp', 'knitr', 'magrittr', 'microbenchmark', 'rmarkdown', 'sf',
  'SpaDES.core', 'testthat'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggnetwork', 'igraph', 'network', 'rlang', 'sf', 'sna'

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: 'meta', 'magic', 'ggplot2', 'metafor'

Packages suggested but not available for checking:
  'colorspace', 'rgl', 'hasseDiagram', 'mvtnorm', 'gridExtra',
  'igraph', 'tictoc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertive', 'devtools', 'dplyr', 'rappdirs', 'readr', 'seqinr',
  'stringr', 'testit', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clue', 'gtools', 'igraph', 'lda', 'poisbinom', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'ergm', 'ggplot2', 'network', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'Hmisc', 'colorspace', 'mvtnorm', 'corpcor', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'network', 'sna'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'igraphdata', 'intergraph',
  'ggraph', 'gridGraphics', 'ggplot2', 'gridExtra', 'gridBase',
  '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: 'graph'

Package suggested but not available for checking: 'bionetdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'magrittr', 'testthat', 'shiny', 'miniUI',
  'rstudioapi'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'knitcitations'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'foreach', 'Rcpp', 'statmod', 'RhpcBLASctl', 'abind', 'RColorBrewer',
  'BH', 'RcppArmadillo'

Packages suggested but not available for checking:
  'bigmemory', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggraph', 'ggplot2', 'igraph'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'magrittr', 'wTO', 'CoDiNA', 'dplyr', 'Rfast', 'binr',
  'BiRewire', 'cubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DiagrammeR', 'DiagrammeRsvg', 'htmlwidgets', 'knitr', 'magrittr',
  'rsvg', 'svglite', 'png', 'segmented', 'gtools'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'crch', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'usethis', 'here', 'httr', 'jsonlite', 'purrr',
  'xml2', 'rvest', 'pbapply'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'RColorBrewer', 'network', 'sna'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'MCMCpack', 'ggplot2', 'Rmpfr', 'abind', 'mvtnorm', 'tidyr',
  'igraph', 'qgraph', 'network', 'RColorBrewer', 'reshape', 'ggrepel',
  'gridExtra', 'rlang', 'GGally', 'ggvis'

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:
  'qgraph', 'IsingFit', 'IsingSampler', 'reshape2'

Package suggested but not available for checking: 'networktools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', 'igraph', 'magrittr'

Packages suggested but not available for checking: 'htmltools', 'jsonlite'

Packages which this enhances but not available for checking:
  'knitr', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'Rdpack', 'RSpectra', 'doParallel', 'foreach', 'graphon',
  'igraph', 'network', 'pracma', 'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'networkDynamic', 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'network', 'statnet.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'magrittr', 'network', 'scales', 'sna',
  'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'pkgdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'assertthat', 'checkmate', 'ggplot2', 'ggrepel',
  'RcppProgress'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'pander', 'igraph', 'dplyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'magrittr', 'statnet.common'

Packages suggested but not available for checking:
  'sna', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'randnet', 'RSpectra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'functional', 'ggplot2', 'lazyeval', 'plyr', 'reshape2', 'stringr',
  'dplyr', 'surveybootstrap'

Packages suggested but not available for checking: 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'expm', 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'igraph', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'data.table', 'fastmatch', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'igraph', 'KFAS', 'limSolve', 'plyr', 'Rglpk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'psych', 'corrplot', 'fdrtool', 'R.matlab', 'igraph', 'qgraph',
  'ppcor', 'foreach', 'doParallel', 'pwr', 'IsingFit', 'pbapply'

Package suggested but not available for checking: 'googledrive'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'qgraph', 'igraph', 'IsingFit', 'reshape2', 'ggplot2', 'gridExtra',
  'NetworkComparisonTest', 'cocor', 'RColorBrewer', 'R.utils',
  'eigenmodel', 'psych', 'smacof', 'wordcloud'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'partykit', 'qgraph', 'mvtnorm', 'Formula', 'gridBase', 'reshape2'

Packages suggested but not available for checking:
  'R.rsp', 'knitr', 'rmarkdown', 'fxregime', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Deriv'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'scales', 'tidyr'

Packages suggested but not available for checking:
  'caret', 'neuralnet', 'RSNNS', '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.
mlptrain : rect: no visible global function definition for 'polygon'
mlptrain : drawnet: no visible global function definition for 'title'
mlptrain : drawnet: no visible global function definition for 'polygon'
mlptrain : drawnet: no visible global function definition for 'text'
mlptrain : drawnet: no visible global function definition for 'lines'
mlptrain: no visible global function definition for 'runif'
mlptrain: no visible global function definition for 'locator'
mlptrain: no visible global function definition for 'polygon'
mlptrain: no visible global function definition for 'text'
rbftrain : rect: no visible global function definition for 'polygon'
rbftrain : drawnet: no visible global function definition for 'title'
rbftrain : drawnet: no visible global function definition for 'polygon'
rbftrain : drawnet: no visible global function definition for 'text'
rbftrain : drawnet: no visible global function definition for 'lines'
rbftrain : graph: no visible global function definition for 'title'
rbftrain : graph: no visible global function definition for 'polygon'
rbftrain : graph: no visible global function definition for 'text'
rbftrain : graph: no visible global function definition for 'lines'
rbftrain : graph: no visible global function definition for 'points'
rbftrain: no visible global function definition for 'runif'
rbftrain: no visible global function definition for 'locator'
rbftrain: no visible global function definition for 'polygon'
rbftrain: no visible global function definition for 'text'
rbftrain: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans lines locator points polygon runif text title
Consider adding
  importFrom("graphics", "lines", "locator", "points", "polygon", "text",
             "title")
  importFrom("stats", "kmeans", "runif")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'gridExtra', 'NeuralNetTools', 'reshape2', 'caret',
  'fastDummies', 'stringr', 'Hmisc', 'ggforce', 'scales', 'ggnewscale',
  'magrittr'

Packages suggested but not available for checking:
  'h2o', 'neural', 'RSNNS', 'neuralnet', 'plotly', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'oro.nifti', 'abind', 'matrixStats', 'R.utils', 'RNifti'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'knitr', 'rmarkdown', 'dplyr', 'reshape2',
  'httr', 'covr', 'brainR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'devtools'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'httr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'httr', 'xml2', 'base64enc', 'aws.s3'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'hash', 'yaImpute', 'Rcpp', 'iterators', 'abind',
  'assertthat', 'readr', 'rgl'

Packages suggested but not available for checking:
  'foreach', 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BayesLogit', 'ggplot2', 'dplyr', 'tidyr', 'magrittr', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'deSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'scales', 'pracma', 'ggpmisc', 'cowplot'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'Rcpp', 'tidyr', 'dplyr', 'purrr', 'tibble', 'forcats',
  'ggplot2', 'rlang', 'magrittr', 'flipr', 'cli', 'withr',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'zoo'

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.
Package required but not available: 'AdequacyModel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ctgt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'oompaBase'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'httr', 'jsonlite', 'tidyr', 'xml2', 'lubridate',
  'askpass'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'magrittr', 'rmarkdown', 'robotstxt', 'rvest',
  'stringr', 'testthat', 'mockery', 'tidytext', 'textdata'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidyRSS'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quanteda', 'quanteda.textstats', 'stringi'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'R6'

Packages suggested but not available for checking:
  'desc', 'knitr', 'lintr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'psych'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
nfca : nFCAmain: no visible global function definition for 'hist'
nfca : nFCAmain: no visible global function definition for
  'flush.console'
nfca : nFCAmain: no visible global function definition for 'qnorm'
nfca : nFCAmain: no visible global function definition for 'read.csv'
nfca : nFCAmain: no visible global function definition for 'cor'
nfca : nFCAmain: no visible global function definition for 'as.dist'
nfca : nFCAmain: no visible global function definition for 'cophenetic'
nfca : nFCAmain: no visible global function definition for 'hclust'
nfca : thresholdTEST: no visible global function definition for
  'read.csv'
nfca : gScript: no visible global function definition for 'read.csv'
nfca : gScript0: no visible global function definition for 'read.csv'
nfca : gMatrix: no visible global function definition for 'read.csv'
nfca: no visible global function definition for 'cor'
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Running examples in 'nFCA-Ex.R' failed
The error most likely occurred in:

> ### Name: nfca
> ### Title: Numerical Formal Concept Analysis for Systematic Clustering
> ### Aliases: nfca
> 
> ### ** Examples
> 
> # View a build-in correlation matrix: nfca_example
> data("nfca_example", package = "nFCA")
> nfca_example
      H    W    S    D   HF   HM   WF   WM   H1   W1    O
1  1.00 0.95 0.90 0.90 0.85 0.85 0.80 0.80 0.40 0.30 0.10
2  0.95 1.00 0.88 0.88 0.70 0.70 0.87 0.87 0.20 0.45 0.15
3  0.90 0.88 1.00 0.82 0.80 0.80 0.76 0.76 0.10 0.10 0.02
4  0.90 0.88 0.82 1.00 0.82 0.82 0.81 0.81 0.10 0.10 0.05
5  0.85 0.70 0.80 0.82 1.00 0.95 0.65 0.65 0.08 0.06 0.01
6  0.85 0.70 0.80 0.82 0.95 1.00 0.60 0.60 0.06 0.07 0.01
7  0.80 0.87 0.76 0.81 0.65 0.60 1.00 0.95 0.03 0.05 0.01
8  0.80 0.87 0.76 0.81 0.65 0.60 0.95 1.00 0.01 0.02 0.01
9  0.40 0.20 0.10 0.10 0.08 0.06 0.03 0.01 1.00 0.02 0.01
10 0.30 0.45 0.10 0.10 0.06 0.07 0.05 0.02 0.02 1.00 0.02
11 0.10 0.15 0.02 0.05 0.01 0.01 0.01 0.01 0.01 0.02 1.00
>      
> # 1. using the default 'histogram' method and choosing threshold
> # automatically   
> nfca(data = nfca_example)
Warning in system("ruby multistagefca.rb") : 'ruby' not found
Warning in file.rename("example.dot", "example.txt") :
  cannot rename file 'example.dot' to 'example.txt', reason 'The system cannot find the file specified'
Warning in file(file, "rt") :
  cannot open file 'example.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: nfca ... thresholdTEST -> as.matrix -> read.csv -> read.table -> file
Execution halted
Packages required but not available:
  'FKF.SP', 'LSMRealOptions', 'numDeriv', 'rgenoud', 'mathjaxr',
  'Rdpack', 'curl'

Packages suggested but not available for checking: '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'
Running 'testthat.R'
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', 'glue', 'httr', 'janitor', 'jsonlite', 'magrittr',
  'nflfastR', 'nflreadr', 'purrr', 'stringr', 'tibble', 'tidyr',
  'tidyselect', 'xgboost'

Packages suggested but not available for checking:
  'future', 'gt', 'rmarkdown', 'tictoc', 'tidyverse', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'curl', 'dplyr', 'fastrmodels', 'furrr', 'future', 'glue',
  'janitor', 'lifecycle', 'nflreadr', 'progressr', 'rlang', 'stringr',
  'tibble', 'tidyr', 'tidyselect', 'xgboost'

Packages suggested but not available for checking:
  'crayon', 'DBI', 'DT', 'gsisdecoder', 'httr', 'jsonlite', 'purrr',
  'qs', 'rmarkdown', 'RSQLite', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'ggplot2', 'magick', 'magrittr', 'nflreadr', 'rlang', 'scales'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggtext', 'gridtext', 'knitr', 'rmarkdown',
  'rstudioapi', 'rsvg', 'sjmisc', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cachem', 'cli', 'curl', 'data.table', 'glue', 'memoise', 'qs',
  'rappdirs', 'Rcpp', 'RcppParallel', 'rlang'

Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'progressr', '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', 'curl', 'dplyr', 'furrr', 'future', 'glue',
  'gsubfn', 'magrittr', 'progressr', 'purrr', 'readr', 'rlang',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'progress'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'crayon', 'magrittr', 'nfl4th', 'nflfastR', 'nflplotR',
  'nflreadr', 'nflseedR', 'rlang', 'rstudioapi'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'graph', 'igraph', 'stringr', 'magrittr', 'plyr', 'ggplot2',
  'apcluster', 'KEGGgraph', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'graphite', 'NFPdata', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'gsl', 'lamW'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running examples in 'NFWdist-Ex.R' failed
The error most likely occurred in:

> ### Name: nfw
> ### Title: The Standard Distribution Functions for the 3D NFW Profile
> ### Aliases: NFW NFWdist nfw dnfw pnfw qnfw rnfw
> ### Keywords: nfw
> 
> ### ** Examples
> 
> #Both the PDF (dnfw) integrated up to x, and CDF at q (pnfw) should be the same:
> #0.373, 0.562, 0.644, 0.712
> 
> for(con in c(1,5,10,20)){
+   print(integrate(dnfw, lower=0, upper=0.5, con=con)$value)
+   print(pnfw(0.5, con=con))
+ }
[1] 0.373455
[1] 0.373455
[1] 0.5618349
[1] 0.5618349
[1] 0.6437556
[1] 0.6437556
[1] 0.7116174
[1] 0.7116174
> 
> #The qnfw should invert the pnfw, returning the input vector (1:9)/10:
> for(con in c(1,5,10,20)){
+   print(qnfw(p=pnfw(q=(1:9)/10,con=con), con=con))
+ }
Using slow internal Lambert W0, ideally you shouls install the lamW or the gsl package.
Packages required but not available:
  'reticulate', 'dplyr', 'forecast', 'magrittr', 'R6'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rfast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', 'magrittr', 'shiny'

Packages suggested but not available for checking:
  'knitr', 'webshot', '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:
  'httr', 'rlang', 'RCurl', 'dplyr', 'cli', 'tibble', 'tidyr', 'rjson',
  'stringr', 'ggplot2', 'scales', 'xml2', 'textutils', 'lifecycle'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tm', 'tau'

Packages suggested but not available for checking: 'testthat', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'batchmeans', 'RcppArmadillo'

Package suggested but not available for checking: 'pbapply'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'interp', 'mvtnorm', 'dlm', 'car'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringr', 'Hmisc', 'rvest', 'magrittr', 'xml2', 'plyr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mosaic'
Packages required but not available:
  'dplyr', 'sf', 'RANN', 'units', 'magrittr', 'jsonlite', 'httr',
  'xml2', 'R.utils', 'tidyr', 'rosm', 'prettymapr', 'fst',
  'dataRetrieval', 'zip', 'pbapply'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'markdown', 'ggmap', 'ggplot2',
  'sp', 'lwgeom', 'devtools', 'data.table', 's2', 'gifski'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'maps', 'rappdirs', 'rgdal', 'sf', 'httr', 'rvest', 'xml2',
  'ggplot2', 'rlang', 'dplyr', 'curl', 'units', 'stringr', 'memoise',
  'purrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'wikilake', 'sp', 'rgeos', 'testthat', 'covr',
  'crul', 'lwgeom', 's2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'RSQLite', 'rvest', 'DBI', 'xml2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BayesLogit', 'msm', 'MCMCpack', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'deSolve', 'maxLik', 'mvtnorm'

Package suggested but not available for checking: 'msm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ucminf', 'lars', 'glasso', 'ncvreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'dplyr', 'magrittr', 'rvest', 'stringr', 'purrr', 'tibble',
  'httr'

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 suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'caret', 'e1071', 'readr', 'magrittr', 'varhandle',
  'rsample', 'ggplot2', 'lme4', 'ModelMetrics', 'lmtest', 'rmarkdown',
  'scales', 'ggrepel', 'lubridate', 'tidyr', 'forcats', 'knitr',
  'janitor', 'stringi', 'synthpop'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'scales', 'dplyr', 'rlang', 'crayon', 'NHSRdatasets',
  'assertthat'

Packages suggested but not available for checking:
  'covr', 'lintr', 'testthat', 'rmarkdown', 'knitr', 'mockery',
  'withr', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'dismo', 'e1071', 'maps', 'pROC', 'randomForest', 'raster',
  'rJava', 'spider', 'vegan'

Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'ape', 'castor', 'concaveman', 'geiger', 'raster', 'rgdal', 'rgeos',
  'sf', 'sp', 'stringr'

Packages suggested but not available for checking: 'knitr', 'phytools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'palmerpenguins', 'rmarkdown', 'tidyverse'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'maps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'raster', 'sp', 'rgdal'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'lpSolve', 'TSP'
Packages required but not available:
  'plotly', 'tidyr', 'bipartite', 'crayon', 'dplyr', 'ggplot2',
  'igraph', 'purrr', 'skimr', 'bnstruct', 'RColorBrewer', 'fpc',
  'mice', 'missMDA', 'networkD3', 'scales', 'softImpute', 'tibble',
  'tidytext', 'visNetwork'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'htmltools', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'ggplot2', 'ggthemes', 'scales', 'gtools', 'dplyr',
  'gridExtra'

Packages suggested but not available for checking:
  'knitr', 'roxygen2', 'testthat', 'tibble', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nimble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'coda'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nimble', 'rcarbon', 'snow', 'doSNOW', 'foreach', 'coda'

Packages suggested but not available for checking:
  'spelling', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nimble'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'igraph', 'coda', 'R6'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nimble'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'coda', 'basicMCMCplots'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nimble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'bbw', 'withr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tufte', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'tibble'

Package suggested but not available for checking: 'RColorBrewer'

Packages which this enhances but not available for checking:
  'kokudosuuchi', 'estatapi', 'jpndistrict', 'jpmesh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rsamtools', 'sets', 'S4Vectors'

Packages suggested but not available for checking: 'knitr', 'pander'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Packages required but not available: 'fdasrvf', 'fda', 'fda.usc'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'dplyr', 'RCurl', 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'zoo', 'car'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'plyr', 'reshape2', 'ggplot2', 'scales',
  'MuMIn', 'rsq'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bpcp', 'ssanv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'zoo', 'lubridate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'jsonlite', 'httr', 'curl', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'rjson', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lubridate', 'httr', 'curl', 'readr', 'dplyr', 'stringr',
  'tidyselect'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rappdirs'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'dplyr', 'magrittr', 'skimr', 'sf', 'maps',
  'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'R.rsp', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quadprog'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'a4Core', 'MLInterfaces', 'xtable', 'limma', 'Biobase', 'multtest',
  'RColorBrewer', 'pamr', 'randomForest', 'ROCR', 'ipred', 'e1071',
  'kernlab'

Packages suggested but not available for checking: 'RUnit', 'ALL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'timeSeries', 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gridExtra', 'gtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'chk', 'coda', 'extras', 'generics', 'lifecycle', 'purrr',
  'term', 'tibble', 'universals'

Packages suggested but not available for checking:
  'covr', 'rlang', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'deSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'Hmisc', 'SASmixed'
Packages suggested but not available for checking:
  'reshape', 'WWGbook', 'ellipse', 'roxygen2', 'testthat'
Malformed Title field: should not end in a period.
Pwr.lme: no visible global function definition for 'anova'
Pwr.lme: no visible global function definition for 'qf'
Pwr.lme: no visible global function definition for 'pf'
logLik1.lme: no visible global function definition for 'coef'
logLik1.lme: no visible global function definition for 'model.matrix'
logLik1.lme: no visible global function definition for 'predict'
logLik1.lme: no visible global function definition for 'formula'
runScript: no visible binding for global variable 'example'
sigmaTolme: no visible global function definition for 'vcov'
simulateY.lme: no visible global function definition for 'runif'
simulateY.lme: no visible global function definition for 'fitted'
simulateY.lme: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
Running 'Pwr1.R'
Running the tests in 'tests/Pwr1.R' failed.
Complete output:
  > date()
  [1] "Sun Mar 27 06:15:38 2022"
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Hmisc', 'magrittr', 'dplyr', 'tidyr', 'quantreg', 'optimx',
  'ggplot2', 'timeDate', 'plyr', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'brew', 'lbfgsb3c', 'dparser', 'ggplot2', 'rex', 'minqa',
  'n1qn1', 'fastGHQuad', 'RxODE', 'magrittr', 'backports', 'symengine',
  'RcppEigen', 'BH', 'StanHeaders', 'RcppArmadillo'

Packages suggested but not available for checking:
  'Deriv', 'Rvmmin', 'broom.mixed', 'crayon', 'knitr', 'data.table',
  'devtools', 'digest', 'dotwhisker', 'dplyr', 'expm', 'flextable',
  'ggtext', 'patchwork', 'gridExtra', 'huxtable', 'lbfgs', 'lotri',
  'madness', 'matrixcalc', 'nloptr', 'officer', 'pkgdown', 'reshape2',
  'rmarkdown', 'testthat', 'tidyr', 'ucminf', 'vpc', 'xgxr', 'yaml',
  'xpose', 'generics', 'tibble', 'checkmate', 'cli', 'qs', 'covr',
  'forecast', 'latticeExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lqmm', 'HI', 'mvtnorm', 'numDeriv', 'statmod', 'Qtools', 'Rcpp',
  'RcppArmadillo', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'minpack.lm', 'optimx', 'Rvmmin', 'Rcgmin', 'numDeriv'
Running examples in 'nlmrt-Ex.R' failed
The error most likely occurred in:

> ### Name: model2grfun
> ### Title: Generate a gradient function from a nonlinear model expression
> ###   and a vector of named parameters.
> ### Aliases: model2grfun
> ### Keywords: nonlinear least squares
> 
> ### ** Examples
> 
>   cat("See also examples in nlmrt-package.Rd\n")
See also examples in nlmrt-package.Rd
>   require(numDeriv)
Loading required package: numDeriv
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'numDeriv'
>   y <- c(5.308, 7.24, 9.638, 12.866, 17.069, 23.192, 31.443, 38.558, 
+       50.156, 62.948, 75.995, 91.972)  # for testing
>   tt <- seq_along(y)  # for testing
>   f <- y ~ b1/(1 + b2 * exp(-1 * b3 * tt))
>   p <- c(b1 = 1, b2 = 1, b3 = 1)
>   mygr <- model2grfun(f, p)
>   myss <- model2ssfun(f, p) # for check
>   cat("mygr:\n")
mygr:
>   print(mygr)
function (prm, y = NULL, tt = NULL) 
{
    b1 <- prm[[1]]
    b2 <- prm[[2]]
    b3 <- prm[[3]]
    localdf <- data.frame(y, tt)
    jstruc <- with(localdf, eval({
        .expr4 <- exp(-1 * b3 * tt)
        .expr6 <- 1 + b2 * .expr4
        .expr11 <- .expr6^2
        .value <- b1/.expr6 - y
        .grad <- array(0, c(length(.value), 3), list(NULL, c("b1", 
            "b2", "b3")))
        .grad[, "b1"] <- 1/.expr6
        .grad[, "b2"] <- -(b1 * .expr4/.expr11)
        .grad[, "b3"] <- b1 * (b2 * (.expr4 * tt))/.expr11
        attr(.value, "gradient") <- .grad
        .value
    }))
    jacmat <- attr(jstruc, "gradient")
    resids <- as.numeric(eval(b1/(1 + b2 * exp(-1 * b3 * tt)) - 
        y))
    grj <- as.vector(2 * crossprod(jacmat, resids))
}
<environment: 0x0000025ddadfab48>
>   
>   ans <- mygr(p, tt = tt, y = y)
>   print(ans)
[1] -824.042084    4.764888  -11.025384
>   gnum <- grad(myss, p, tt = tt, y = y)
Error in grad(myss, p, tt = tt, y = y) : could not find function "grad"
Execution halted
Error(s) in re-building vignettes:
--- re-building 'nlmrt-vignette.Rnw' using Sweave
Loading required package: nlmrt
Error in nlsModel(formula, mf, start, wts, scaleOffset = scOff, nDcentral = nDcntr) : 
  singular gradient matrix at initial parameter estimates
Error in nls(regmod, start = huetstart, trace = FALSE, data = pastured) : 
  singular gradient
Loading required package: optimx
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'optimx'

Error: processing vignette 'nlmrt-vignette.Rnw' failed with diagnostics:
 chunk 10 (label = chunk10) 
Error in optimx(st, shobbs.f, shobbs.g, control = list(all.methods = TRUE)) : 
  could not find function "optimx"

--- failed re-building 'nlmrt-vignette.Rnw'

SUMMARY: processing the following file failed:
  'nlmrt-vignette.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ROCR', 'TSP', 'igraph', 'fdrtool', 'coin', 'earth', 'randomForest',
  'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'testthat'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'xml2', '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: 'NLP', 'xml2', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'udpipe', 'spacyr', 'cleanNLP'
Packages unavailable to check Rd xrefs: 'tm', 'udpipe', 'spacyr', 'cleanNLP'
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  'data.table', 'SuperLearner', 'cvAUC', 'ROCR', 'Rdpack', 'bde', 'np',
  'assertthat'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'prettydoc', 'randomForest',
  'ranger', 'xgboost', 'glmnet'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'NLP', 'SnowballC', 'qdap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'knitr'

Packages suggested but not available for checking:
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  'nlstools', 'nls2', 'rmarkdown', 'segmented'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rms', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'XML', 'lhs', 'sensitivity', 'dplyr', 'readr', 'purrr', 'furrr',
  'magrittr', 'GenSA', 'genalg', 'raster', 'rstudioapi', 'sf', 'tidyr',
  'tibble', 'crayon', 'igraph', 'stringr', 'progressr', 'EasyABC'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'proto'

Package suggested but not available for checking: 'nlstools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'orthopolynom', 'lavaan', 'gaussquad', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'dplyr', 'magicaxis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nloptr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nnls'

Packages suggested but not available for checking:
  'numDeriv', 'RUnit', 'limSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nlstools'

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:
  'minpack.lm', 'purrr', 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'broom', 'nlstools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'digest'

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  'minpack.lm', 'optimx', 'numDeriv', 'knitr', 'rmarkdown', 'markdown',
  'Ryacas', 'Deriv'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Deriv', 'doParallel', 'foreach', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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  'knitr', 'rmarkdown', 'rticles'

VignetteBuilder package required for checking but not installed: 'knitr'
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manual.
Packages required but not available: 'locfit', 'acepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ape', 'coda', 'testit'

Packages suggested but not available for checking:
  'DDD', 'ggplot2', 'Hmisc', 'knitr', 'lintr', 'microbenchmark',
  'plyr', 'reshape2', 'rmarkdown', 'TESS', 'testthat', 'TreeSim',
  'DAISIE'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'RCurl', 'readxl', 'jsonlite'

Packages suggested but not available for checking: 'netmeta', 'V8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjags', 'coda', 'ggplot2', 'ks', 'reshape2', 'MCMCpack', 'plotrix',
  'imguR', 'Rdpack'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
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  'INLA', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/nmaINLA.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/nmaINLA.Rnw'
(Is a VignetteBuilder field missing?)
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'netmeta', 'meta', 'reshape2', 'ggplot2', 'gridExtra'

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', 'svglite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'meta', 'netmeta', 'data.tree', 'mvtnorm', 'tidyr', 'dplyr',
  'tibble', '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:
  'nnls', 'gridExtra', 'gtable', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'coda'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'formatR', 'mime', 'rmarkdown', 'ggplot2',
  'tibble', 'covr', 'htmltools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
nnmf_als: no visible global function definition for 'rnorm'
nnmf_mm: no visible global function definition for 'rnorm'
nnmf_prob: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Packages required but not available:
  'pkgmaker', 'registry', 'rngtools', 'stringr', 'digest', 'gridBase',
  'colorspace', 'RColorBrewer', 'foreach', 'doParallel', 'ggplot2',
  'reshape2', 'BiocManager', 'Biobase'

Packages suggested but not available for checking:
  'fastICA', 'doMPI', 'bigmemory', 'synchronicity', 'corpcor',
  'xtable', 'devtools', 'knitr', 'bibtex', 'RUnit', 'mail'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/NMF-vignette.Rnw'
   'inst/doc/heatmaps.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'magrittr', 'purrr', 'rappdirs', 'rlang', 'tibble',
  'tidyselect', 'stringr'

Packages suggested but not available for checking:
  'lubridate', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'unmarked'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lava', 'nloptr', 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'systemfit', 'DEoptim', 'data.table', 'magrittr', 'maxLik', 'Rdpack',
  'AER', 'mlogit', 'Hmisc', 'gsubfn', 'abind', 'tidyr', 'plyr', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'recipes', 'Stat2Data'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'PMwR', 'RUnit', 'Rglpk', 'datetimeutils', 'openxlsx', 'quadprog',
  'readxl', 'tinytest'
Packages unavailable to check Rd xrefs: 'PMwR', 'Rglpk', 'quadprog'
Running examples in 'NMOF-Ex.R' failed
The error most likely occurred in:

> ### Name: mvFrontier
> ### Title: Computing Mean-Variance Efficient Portfolios
> ### Aliases: mvFrontier mvPortfolio
> 
> ### ** Examples
> 
> na <- 4
> vols <- c(0.10, 0.15, 0.20,0.22)
> m <- c(0.06, 0.12, 0.09, 0.07)
> const_cor <- function(rho, na) {
+     C <- array(rho, dim = c(na, na))
+     diag(C) <- 1
+     C
+ }
> var <- diag(vols) %*% const_cor(0.5, na) %*% diag(vols)
> 
> wmax <- 1          # maximum holding size
> wmin <- 0.0          # minimum holding size
> rf <- 0.02
> 
> p1 <- mvFrontier(m, var, wmin = wmin, wmax = wmax, n = 50)
Loading required namespace: quadprog
Failed with error:  'there is no package called 'quadprog''
Error in mvFrontier(m, var, wmin = wmin, wmax = wmax, n = 50) : 
  package 'quadprog' is not available
Execution halted
Errors in running code in vignettes:
when running code in 'portfolio.Rnw'

> options(continue = "  ", digits = 3, width = 60, useFancyQuotes = FALSE, 
+     max.print = 1000, width = 65)

> pv <- packageVersion("NMOF")

> pv <- gsub("(.*)[.](.*)", "\\1-\\2", pv)

> library("NMOF")

> var <- structure(c(0.000988087100677907, -1.79669410403153e-05, 
+     0.000368923882626859, 0.000208303611101873, 0.000262742052359594, 
+     -1.7 .... [TRUNCATED] 

> var
           CBK.DE    VOW.DE   CON.DE   LIN.DE  MUV2.DE
CBK.DE   0.000988 -1.80e-05 3.69e-04 2.08e-04 2.63e-04
VOW.DE  -0.000018  1.72e-03 8.57e-05 2.15e-05 2.84e-05
CON.DE   0.000369  8.57e-05 7.59e-04 1.94e-04 1.89e-04
LIN.DE   0.000208  2.15e-05 1.94e-04 2.66e-04 1.33e-04
MUV2.DE  0.000263  2.84e-05 1.89e-04 1.33e-04 2.59e-04

> minvar(var, wmin = 0, wmax = 0.5)
Loading required namespace: quadprog
Failed with error:  'there is no package called 'quadprog''

  When sourcing 'portfolio.R':
Error: package 'quadprog' is not available
Execution halted

  'An_overview.Rnw'... OK
  'DEnss.Rnw'... OK
  'LSqueens.Rnw'... OK
  'LSselect.Rnw'... OK
  'PSlms.Rnw'... OK
  'TAportfolio.Rnw'... OK
  'portfolio.Rnw'... failed
  'qTableEx.Rnw'... OK
  'repair.Rnw'... OK
  'vectorise.Rnw'... OK
Error(s) in re-building vignettes:
--- re-building 'An_overview.Rnw' using Sweave
found several files...
--- finished re-building 'An_overview.Rnw'

--- re-building 'DEnss.Rnw' using Sweave
--- finished re-building 'DEnss.Rnw'

--- re-building 'LSqueens.Rnw' using Sweave
--- finished re-building 'LSqueens.Rnw'

--- re-building 'LSselect.Rnw' using Sweave
--- finished re-building 'LSselect.Rnw'

--- re-building 'PSlms.Rnw' using Sweave
--- finished re-building 'PSlms.Rnw'

--- re-building 'TAportfolio.Rnw' using Sweave
--- finished re-building 'TAportfolio.Rnw'

--- re-building 'portfolio.Rnw' using Sweave
Loading required namespace: quadprog
Failed with error:  'there is no package called 'quadprog''

Error: processing vignette 'portfolio.Rnw' failed with diagnostics:
 chunk 5 (label = minvar) 
Error in minvar(var, wmin = 0, wmax = 0.5) : 
  package 'quadprog' is not available

--- failed re-building 'portfolio.Rnw'

--- re-building 'qTableEx.Rnw' using Sweave
--- finished re-building 'qTableEx.Rnw'

--- re-building 'repair.Rnw' using Sweave
--- finished re-building 'repair.Rnw'

--- re-building 'vectorise.Rnw' using Sweave
--- finished re-building 'vectorise.Rnw'

SUMMARY: processing the following file failed:
  'portfolio.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'shiny', 'reshape2', 'dygraphs', 'DT', 'git2r', 'dplyr', 'stringr',
  'rlang', 'diffobj', 'tidyr', 'miniUI', 'rstudioapi', 'crayon',
  'rprojroot', 'htmltools', 'rmarkdown', 'magrittr', 'usethis',
  'lifecycle'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ggplot2', 'future', 'data.tree', 'xpose',
  'lubridate', 'pmxTools', 'Hmisc', 'rsample', 'renv', 'desc', 'purrr',
  'digest', 'covr', 'devtools', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'reticulate', 'R6', 'KernelKnn', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'R6', 'pkgload'

Packages suggested but not available for checking: 'brnn', 'validann'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RSNNS'

Package suggested but not available for checking: 'neuralnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'forecast', 'glmnet', 'neuralnet', 'plotrix', 'tsutils', 'uroot'

Package suggested but not available for checking: 'thief'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'glmnet'

Packages suggested but not available for checking: 'testthat', 'mvnfast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'nabor', 'units', 'lwgeom', 's2', 'data.table'

Packages suggested but not available for checking:
  'DBI', 'RPostgreSQL', 'stars', 'knitr', 'rmarkdown', 'tinytest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages unavailable to check Rd xrefs: 'quadprog', 'bvls'
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rdpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'doParallel', 'caret', 'data.table', 'dtw', 'dynlm', 'meboot',
  'Quandl', 'Rfast', 'rgl', 'stringr', 'tdigest', 'tseries', '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:
  'shiny', 'xtable', 'stringr', 'magrittr', 'mvbutils'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'plyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'rTensor', 'plot3D', 'tagcloud', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'survRM2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'NeuralNetTools', 'FNN', 'pracma'

Packages suggested but not available for checking:
  'dplyr', 'knitr', 'rmarkdown', 'ggplot2', 'ggridges', 'tidyr',
  'forcats', 'mlr', 'mlrCPO'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'rvest', 'xml2'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'dplyr', 'httptest',
  'ggplot2', 'maps', 'mapdata'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'choroplethr', 'choroplethrMaps', 'data.table', 'dplyr', 'forcats',
  'ggplot2', 'hurricaneexposure', 'lubridate', 'maps', 'magrittr',
  'plyr', 'RColorBrewer', 'RCurl', 'rlang', 'stringr', 'tibble',
  'tidyr', 'viridis', 'XML'

Packages suggested but not available for checking:
  'hurricaneexposuredata', 'knitr', 'pander', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'hash', 'digest', 'assertthat', 'purrr', 'dplyr', 'magrittr',
  'crayon', 'rlang', 'stringr'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rjags', 'coda', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'DBI', 'paws', 'uuid'

Packages suggested but not available for checking:
  'arrow', 'bit64', 'dplyr', 'dbplyr', 'readr', 'testthat', 'tibble',
  'vroom', 'covr', 'knitr', 'rmarkdown', 'jsonify', 'jsonlite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stringi', 'jsonlite', 'jsonify', 'uuid', 'jqr', 'sofa', 'elastic',
  'mongolite', 'RSQLite', 'RPostgres', 'DBI'

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', 'igraph', 'word2vec', 'rlist', 'dplyr', 'vctrs',
  'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quadprog', 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RPANDA', 'nLTT', 'apTreeshape', 'phangorn', 'tibble', 'DDD',
  'Rmpfr', 'assertthat', 'pbapply', 'phylobase', 'geiger', 'ape',
  'babette', 'beautier', 'beastier', 'mauricer', 'tracerer',
  'rappdirs', 'testit', 'stringr'

Packages suggested but not available for checking:
  'phytools', 'testthat', 'TreeSim', 'dplyr', 'knitr', 'rmarkdown',
  'ggplot2', 'magrittr', '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:
  'picante', 'raster', 'ape', 'sp', 'vegan'

Packages suggested but not available for checking:
  'RColorBrewer', 'testthat', 'colorspace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rlang'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RWeka', 'kknn', 'caret', 'e1071', 'randomForest', 'rJava'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/NoiseFiltersR.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'preprocessCore'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magrittr'

Packages suggested but not available for checking: 'coda', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'dplyr', 'magrittr', 'ggplot2', 'preprocessCore',
  'IRanges', 'GenomicRanges', 'Rsamtools', 'philentropy', 'doParallel',
  'foreach'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gtools', 'ggplot2', 'RColorBrewer'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fracture'

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: 'mirt', 'gmodels'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'jsonlite', 'rlang', 'sf', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'osmdata', 'rmarkdown', 'testthat',
  'tidygeocoder'

VignetteBuilder 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', 'dplyr', 'httr', 'rsdmx', 'rlang', 'snakecase'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'purrr', 'tidyr', 'magrittr',
  'ggplot2', 'scales', '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:
  'htmlwidgets', 'png', 'webshot', 'lifecycle', 'rlang'

Packages suggested but not available for checking:
  'V8', 'knitr', 'rmarkdown', 'testthat', 'shinytest', 'covr',
  'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pracma', 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rms', 'do', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'Rcpp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MCMCpack'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'dplyr', 'randomForest', 'ggplot2', 'rlist', 'glmnet',
  'tidyverse', 'e1071', 'purrr', 'pROC', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ClusterR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CondIndTests', 'data.tree', 'caTools', 'randomForest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'tsDyn', 'minpack.lm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tseries', 'zoo', 'Rcpp', 'lifecycle', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rgl', 'plot3D', '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', 'gridExtra', 'mvtnorm', 'latticeExtra', 'splines2',
  'reshape2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'xml2', 'encode', 'csv', 'spec', 'lazyeval',
  'metaplot', 'magrittr', 'rlang'

Packages suggested but not available for checking:
  'pander', 'knitr', 'wrangle', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'CompQuadForm', 'mvtnorm', 'lavaan', 'sandwich'

Packages suggested but not available for checking:
  'mirt', 'AER', 'faraway', 'mlogit', 'ordinal', 'pscl', 'knitr',
  'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'

Package suggested but not available for checking: 'gtools'

Depends: includes the non-default packages:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'progress'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'gtools', 'pracma', 'colorspace', 'doParallel', 'foreach', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'caret', 'sampling', 'e1071', 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'metafor', 'MCMCglmm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mlogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'copula'
Note: found 3 marked UTF-8 strings
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'odbc', 'DBI', 'magrittr', 'RSQLite', 'writexl',
  'httr', 'jsonlite', 'vcr', 'progressr'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'pscl', 'GIGrvg', 'truncnorm', 'pracma', 'HyperbolicDist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'optimx', 'histogram'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'DT', 'ggplot2', 'rio', 'shiny', 'shinyalert', 'shinyBS',
  'stringi', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DistributionUtils', 'GeneralizedHyperbolic'

Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'purrr', 'magrittr', 'rlang', 'shiny'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rootSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lcmm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable 'var'
mi.inference: no visible global function definition for 'qt'
mi.inference: no visible global function definition for 'pt'
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
ajb.norm.test: no visible global function definition for 'rnorm'
frosini.norm.test: no visible global function definition for 'var'
frosini.norm.test: no visible global function definition for 'pnorm'
frosini.norm.test: no visible global function definition for 'rnorm'
geary.norm.test: no visible global function definition for 'rnorm'
hegazy1.norm.test: no visible global function definition for 'var'
hegazy1.norm.test: no visible global function definition for 'qnorm'
hegazy1.norm.test: no visible global function definition for 'rnorm'
hegazy2.norm.test: no visible global function definition for 'var'
hegazy2.norm.test: no visible global function definition for 'qnorm'
hegazy2.norm.test: no visible global function definition for 'rnorm'
jb.norm.test: no visible global function definition for 'rnorm'
kurtosis.norm.test: no visible global function definition for 'rnorm'
skewness.norm.test: no visible global function definition for 'rnorm'
spiegelhalter.norm.test: no visible global function definition for
  'rnorm'
wb.norm.test: no visible global function definition for 'qnorm'
wb.norm.test: no visible global function definition for 'var'
wb.norm.test: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
normality.test1: no visible global function definition for 'cov.wt'
normality.test1: no visible global function definition for 'cor'
normality.test1: no visible global function definition for 'pnorm'
normality.test1: no visible global function definition for 'pchisq'
normality.test2: no visible global function definition for 'cov.wt'
normality.test2: no visible global function definition for 'cor'
normality.test2: no visible global function definition for 'acf'
normality.test2: no visible global function definition for 'pnorm'
normality.test2: no visible global function definition for 'pchisq'
whitenoise.test: no visible global function definition for 'acf'
whitenoise.test: no visible global function definition for 'spec.pgram'
whitenoise.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  acf cor cov.wt pchisq pnorm spec.pgram
Consider adding
  importFrom("stats", "acf", "cor", "cov.wt", "pchisq", "pnorm",
             "spec.pgram")
to your NAMESPACE file.
Package required but not available: 'astsa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'forecast', 'nortest', 'ggplot2', 'gridExtra', 'tseries', 'uroot',
  'zoo'

Package suggested but not available for checking: 'ggfortify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'raster'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'igraph', 'tidyverse', 'ggplot2',
  'ggnetwork', 'intergraph', 'viridis', 'gifski', 'png', 'gganimate',
  'ape', 'tidytree', 'treeio', 'ggtree', 'magrittr', 'dplyr', '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', 'gmp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'txtplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'dplyr', 'httr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RCurl', 'rjson'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'brms', 'testthat'
Running examples in 'novelforestSG-Ex.R' failed
The error most likely occurred in:

> ### Name: download_model
> ### Title: Download Model Fitted to the 'novelforest' Data
> ### Aliases: download_model
> 
> ### ** Examples
> 
> novelforest_model <- download_model()
To save the model locally, use argument save_to = 'path/filename.rds'
Downloading model (size: 16.5 Mb)
> 
> # library(brms)  # recommended
> summary(novelforest_model)
Loading required package: rstan
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rstan'
Error in .requirePackage(package) : 
  unable to find required package 'rstan'
Calls: summary ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'matlab', 'pracma', 'signal'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'corpcor', 'httr', 'lubridate', 'matlab', 'RCurl', 'xts', 'zoo',
  'DBI', 'magic', 'RMySQL', 'vars'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
.newReportId : <anonymous>: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'stringr', 'zoo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'multcomp', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Packages required but not available:
  'matrixStats', 'matrixcalc', 'gtools', 'Formula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TH.data'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rlang', 'reshape2', 'ggplot2', 'dplyr', 'bayesplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Benchmarking', 'np', 'quadprog', 'Rglpk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BB', 'R.methodsS3'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'circular', 'misc3d', 'movMF', 'plotrix', 'rgl', 'shape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'copula', 'sandwich'
Package unavailable to check Rd xrefs: 'sandwich'
Packages required but not available: 'permute', 'dplyr', 'coin', 'matlab'

Packages suggested but not available for checking:
  'car', 'mvtnorm', 'plyr', 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dfoptim', 'randomForest', 'e1071', 'magrittr', 'smotefamily',
  'foreach', 'naivebayes', 'caret', 'formatR'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'permute', 'zoo'

Package suggested but not available for checking: 'KMsurv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'scales', 'ggplot2', 'mclust', 'gridExtra', 'testthat', 'rlang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'truncnorm', 'ellipse', 'fastcluster', 'ggplot2', 'pheatmap',
  'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'foreach', 'doParallel', 'itertools', 'microbenchmark'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'smcure'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'zoo'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'shiny', 'shinycssloaders', 'formatR', 'styler', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ez', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'RUnit', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/nplr.Rnw'
(Is a VignetteBuilder field missing?)
Files named as vignettes but with no recognized vignette engine:
   'vignettes/nplr.Rnw'
(Is a VignetteBuilder field missing?)
Packages required but not available:
  'Rmosek', 'R.utils', 'dplyr', 'spatstat', 'latexpdf', 'FDRreg',
  'Rcpp', 'REBayes', 'CAMAN', 'progress', 'pbapply', 'Hmisc', 'pracma',
  'mosaic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'statmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'crayon', 'cli', 'erratum'

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 suggested but not available for checking: 'testthat'
Packages required but not available:
  'raster', 'ks', 'rgdal', 'lubridate', 'snow'

Package suggested but not available for checking: 'rgeos'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'anytime', 'futile.logger', 'htmlTable', 'lubridate', 'plotrix',
  'readxl', 'Rlabkey', 'rlang', 'shiny', 'stringi', 'WriteXLS'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'kableExtra', 'knitr', 'markdown',
  'pkgdown', 'png', 'rmarkdown', 'roxygen2', 'shinyBS', 'shinyWidgets',
  'testthat'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cubature', 'quadprog', 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'zoo', 'SPEI', 'WASP', 'knitr', 'ggplot2', 'synthesis', 'testthat',
  'bookdown', '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:
  'shiny', 'doParallel', 'foreach', 'sfsmisc', 'shinyjs',
  'wesanderson', 'ggplot2'

Package suggested but not available for checking: 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'ggplot2', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'glmnet', 'e1071', 'randomForest', 'naivebayes', 'ada', 'ROCR',
  'tree'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'foreach'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'Rcpp'

Packages suggested but not available for checking: 'snowFT', 'Rmpi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
nps.test: no visible global function definition for 'qnorm'
nps.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
Packages required but not available: 'infotheo', 'gmp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for 'mclapply'
Undefined global functions or variables:
  mclapply
Package required but not available: 'lsei'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tidyverse', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'doParallel', 'matrixcalc', 'StepwiseTest', 'foreach', 'mvtnorm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crul', 'xml2'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'CCA', 'glmnet', 'PMA', 'roxygen2', 'testthat'
Package suggested but not available for checking: 'testthat'
Packages required but not available:
  'httr', 'jsonlite', 'magrittr', 'rvest', 'xml2'

Packages suggested but not available for checking:
  'covr', 'DT', 'httptest', 'shiny', 'shinyBS', 'shinycssloaders',
  'shinythemes', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'coda', 'mcmc', 'mcmcse', 'np', 'sandwich'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'magrittr', 'rvest', 'tidyverse', 'stringr', 'jsonlite',
  'RSelenium', 'googleVis', 'dplyr', 'lubridate', 'purrr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'knitr', 'reshape2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'knitr', 'plyr', 'ggplot2', 'lazyeval',
  'stringr'
Package unavailable to check Rd xrefs: 'lazyeval'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'mco'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mlr', 'parallelMap', 'rPref', 'xgboost'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'NSM3'
Packages required but not available:
  'combinat', 'partitions', 'agricolae', 'ash', 'binom', 'BSDA',
  'coin', 'fANCOVA', 'gtools', 'Hmisc', 'km.ci', 'metafor', 'nortest',
  'np', 'quantreg', 'Rfit', 'SemiPar', 'SuppDists', 'waveslim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lsei'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lpSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Package required but not available: 'sde'

Package suggested but not available for checking: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'digest'

Packages suggested but not available for checking:
  'covr', 'DT', 'knitr', 'rmarkdown', 'testthat', 'xml2', 'rvest',
  'readr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'vegan', 'permute', 'ape', 'bigmemory', 'iCAMP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'knitr', 'testthat', 'spelling'
Note: found 1 marked UTF-8 string
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dlm', 'MSwM', 'Rdpack', 'tensor'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'EBImage', 'bioimagetools', 'fields', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'snowfall'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'moments', 'fpc', 'tsibble', 'forecast', 'ggplot2', 'dplyr',
  'purrr', 'tidyr', 'tibble', 'magrittr', 'viridis'

Packages suggested but not available for checking: 'reshape2', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'stringr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gmp'
Running examples in 'numbers-Ex.R' failed
The error most likely occurred in:

> ### Name: Bernoulli numbers
> ### Title: Bernoulli Numbers
> ### Aliases: bernoulli_numbers
> 
> ### ** Examples
> 
> bernoulli_numbers(3); bernoulli_numbers(3, big=TRUE)
     [,1] [,2]
[1,]    1    1
[2,]    1    2
[3,]    1    6
[4,]    0    1
Error: Package 'gmp' needed: Please install separately.
Execution halted
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder 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: 'glue'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'shiny'

Packages suggested but not available for checking:
  'RUnit', 'knitr', 'BiocStyle', 'rmarkdown', 'BiocGenerics'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'stringr', 'testthat', 'tibble', 'tidyr', 'tidyselect',
  'ggplot2', 'dplyr', 'jsonlite', 'qpdf'

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: 'igraph', 'glasso', 'huge', 'tmvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'grpreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'pracma'

Packages suggested but not available for checking:
  'bookdown', 'covr', 'geosphere', 'knitr', 'png', 'rmarkdown',
  'spelling', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'rsvg', 'grImport2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'qrng', 'copula', 'pcaPP', 'ADGofTest', 'mnormt', 'pracma'

Packages suggested but not available for checking:
  'RColorBrewer', 'qrmdata', 'xts', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'knitr', 'rmarkdown', 'ggplot2',
  'scales', 'ggthemes', 'GGally', 'maps', 'mapproj', 'forcats'

VignetteBuilder package required for checking but not installed: 'knitr'
Note: found 6409 marked UTF-8 strings
Running examples in 'nzelect-Ex.R' failed
The error most likely occurred in:

> ### Name: GE2014
> ### Title: General Election Results 2014
> ### Aliases: GE2014
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # the following matches the results published at
> # http://www.electionresults.govt.nz/electionresults_2014/e9/html/e9_part1.html
> library(tidyr)
Error in library(tidyr) : there is no package called 'tidyr'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'curl', 'httr', 'stringi', 'xml2'

Packages suggested but not available for checking:
  'devtools', 'knitr', 'rmarkdown', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'httr', 'stringr', 'rstudioapi'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 7284 marked UTF-8 strings
Packages required but not available:
  'Rcpp', 'geosphere', 'ggplot2', 'visNetwork', 'data.table',
  'outbreaker2'

Packages suggested but not available for checking:
  'testthat', 'tigris', 'sf', 'knitr', 'socialmixr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'magrittr', 'ggplot2', 'ggrepel', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'curl', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xml2', 'httr', 'plyr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'DBI', 'knitr', 'RSQLite', '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: 'oaColors', 'ggplot2'

Package suggested but not available for checking: 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'igraph', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'oaqc_test.R'
Running the tests in 'tests/oaqc_test.R' failed.
Complete output:
  > stopifnot(require('oaqc'), require('igraph'),  getRversion() >= '3.4')
  Loading required package: oaqc
  Loading required package: igraph
  Error: require("igraph") is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'igraph'
  Execution halted
Packages required but not available:
  'rgdal', 'rgeos', 'spdep', 'measurements', 'seg', 'outliers'

Packages suggested but not available for checking: 'testthat', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Formula', 'ggplot2', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'zoo', 'ggplot2', 'reshape2'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'modeest', 'cubature', 'truncdist', 'invgamma', 'LaplacesDemon',
  'HDInterval', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rfast', 'matrixStats', 'stringr', 'readr', 'tibble', 'crayon'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'objectSignals'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'shiny', 'miniUI'

Package suggested but not available for checking: 'rstudioapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Signal.gen: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'ROCR', 'pls', 'mda', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'pec', 'data.table', 'missForest', 'purrr', 'glmnet',
  'dplyr', 'rlang', 'prodlim', 'ggthemes', 'tidyr', 'ggplot2',
  'scales', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
IBMD: no visible global function definition for 'runif'
IBMD: no visible global function definition for 'quantile'
RAI: no visible global function definition for 'runif'
RAI: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile runif
Consider adding
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Packages required but not available: 'svDialogs', 'AGread'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bazar', 'bit', 'dplyr', 'lazyeval', 'magrittr', 'tibble'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
obsSensCCC: no visible global function definition for 'coef'
obsSensCCC: no visible global function definition for 'confint'
obsSensCCN: no visible global function definition for 'coef'
obsSensCCN: no visible global function definition for 'confint'
obsSensCNN: no visible global function definition for 'coef'
obsSensCNN: no visible global function definition for 'confint'
obsSensCNN: no visible global function definition for 'sd'
obsSensCNN: no visible global function definition for 'model.matrix'
obsSensNNN: no visible global function definition for 'coef'
obsSensNNN: no visible global function definition for 'confint'
obsSensNNN: no visible global function definition for 'sd'
obsSensNNN: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  coef confint model.matrix sd
Consider adding
  importFrom("stats", "coef", "confint", "model.matrix", "sd")
to your NAMESPACE file.
Packages required but not available:
  'bib2df', 'BIEN', 'curl', 'dplyr', 'lubridate', 'rgbif', 'taxize',
  'stringr', 'leaflet', 'htmltools', 'ggplot2', 'rlang', 'httr',
  'tidyr', 'RPostgreSQL', 'RColorBrewer', 'viridis', 'DBI', 'waffle'

Packages suggested but not available for checking:
  'rmarkdown', 'remotes', 'RefManageR', 'testthat', 'covr', 'ape',
  'bit64', 'knitr'

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: 'matrixStats'

Packages suggested but not available for checking:
  'VGAM', 'ggplot2', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'sp', 'rgdal', 'broom', 'rgeos', 'ggplot2', 'maps', 'spData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinyBS', 'classInt', 'sf', 'shinyjs', 'shinythemes', 'DT',
  'stringr', 'leaflet', 'leaflet.extras', 'ggplot2', 'dplyr', 'lwgeom',
  'mapview', 'zip'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'markdown', 'rio'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'maps', 'mapdata', 'raster', 'extrafont', 'abind', 'fields',
  'plotrix', 'maptools', 'sp', 'ncdf4', 'lubridate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plot3D', 'plot3Drgl', 'rgl', 'shape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'bspec', 'signal'

Packages suggested but not available for checking:
  'scales', 'oce', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package 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: 'gsw', 'Rcpp'

Packages suggested but not available for checking:
  'akima', 'automap', 'DBI', 'knitr', 'lubridate', 'marmap', 'ncdf4',
  'ocedata', 'raster', 'rgeos', 'rmarkdown', 'RSQLite', 'R.utils',
  'sf', 'sp', 'testthat', 'tiff', 'XML'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'flexclust', 'modeltools'

Package suggested but not available for checking: 'seriation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'entropy', 'mclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'spam', 'rgl', 'igraph', 'SSN', 'rgdal', 'sp'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'bookdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coda', 'bayesm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'R6', 'openssl', 'curl', 'httr', 'jsonlite', 'XML', '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: 'usethis', 'purrr', 'httr'

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: 'R6', 'httr', 'jsonlite', 'rlang'

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: 'XML', 'RJSONIO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bit64', 'blob', 'DBI', 'hms', 'rlang', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'DBItest', 'magrittr', 'RSQLite', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DBI', 'RJDBC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Packages required but not available:
  'caret', 'mlbench', 'magrittr', 'ggplot2', 'tibble', 'ggthemes',
  'e1071', 'tidymodels', 'rmarkdown'

Packages suggested but not available for checking:
  'knitr', 'covr', 'testthat', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pcaPP', 'ggplot2', 'ks', 'RcppRoll', 'moments', 'RColorBrewer',
  'mvtsplot', 'tibble', 'reshape', 'dplyr', 'tidyr', 'kernlab',
  'magrittr'

Packages suggested but not available for checking: 'testthat', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'magrittr', 'dplyr', 'zoo', 'tidyr'

Package suggested but not available for checking: 'morse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'BH'

Packages suggested but not available for checking: 'testthat', 'BH'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'checkmate', 'deSolve'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'deSolve', 'ODEnetwork', 'sensitivity'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'cinterpolate', 'deSolve', 'digest', 'glue', 'jsonlite',
  'ring', 'withr'

Packages suggested but not available for checking:
  'dde', 'jsonvalidate', 'knitr', 'mockery', 'pkgbuild', 'pkgload',
  'rlang', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gsheet', 'openxlsx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'geosphere', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'forecast', 'doParallel', 'foreach', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sfheaders'

Packages suggested but not available for checking:
  'sf', 'knitr', 'rmarkdown', 'tinytest', 'covr', 'lwgeom'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'markdown'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'knitr', 'markdown'
Package required but not available: 'cubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'readsdmx', 'xml2'

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'testthat', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Deriv', 'ggplot2', 'matrixcalc', 'minpack.lm', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigmemory', 'Rcpp', 'foreach', 'RcppEigen', 'BH', 'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'XML'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'minpack.lm', 'openxlsx', 'ggtext', 'extrafont'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'rmarkdown', 'officer', 'xml2', 'rlang', 'uuid', 'yaml',
  'memoise', 'rvg'

Packages suggested but not available for checking:
  'ggplot2', 'flextable', 'bookdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'zip', 'uuid', 'xml2'

Packages suggested but not available for checking:
  'testthat', 'devEMF', 'ggplot2', 'rmarkdown', 'base64enc', 'knitr',
  'rsvg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CompQuadForm', 'forestplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lpSolve'

Packages suggested but not available for checking:
  'ade4', 'bnlearn', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'maxLik'

Packages suggested but not available for checking: 'glmx', 'lmtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'maxLik', 'magrittr', 'dplyr'

Packages suggested but not available for checking:
  'rlang', 'tidyr', 'forcats', 'microbenchmark', 'testthat',
  'numDeriv', 'ggplot2', 'scales', 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'edmdata', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'pls', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rapportools', 'gmodels', 'Deducer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ICS', 'ICSNP', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'rvest', 'tidyr', 'urltools', 'xml2', 'purrr',
  'rlang'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'tidyverse'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'FNN'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'broom', 'dplyr', 'emmeans', 'forcats', 'generics', 'ggplot2',
  'ggpubr', 'ggrepel', 'lme4', 'lmerTest', 'magrittr', 'readxl',
  'rlang', 'stringr', 'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'extrafont', 'knitr', 'rmarkdown', 'testthat', 'scales', 'markdown',
  'vdiffr'

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', 'ggamma'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'knitr', 'lavaan'
OLScurve: no visible global function definition for 'as.formula'
OLScurve: no visible global function definition for 'na.omit'
OLScurve: no visible global function definition for 'lm'
OLScurve: no visible global function definition for 'predict'
OLScurve: no visible global function definition for 'residuals'
OLScurve: no visible global function definition for 'model.frame'
OLScurve: no visible global function definition for 'model.matrix'
plot.OLScurve : plotOLScurve: no visible global function definition for
  'reshape'
print.OLScurve: no visible global function definition for 'na.omit'
print.OLScurve: no visible global function definition for 'model.frame'
print.OLScurve: no visible global function definition for
  'model.matrix'
print.OLScurve: no visible global function definition for 'cov'
print.OLScurve: no visible global function definition for 'cor'
print.OLScurve: no visible global function definition for 'sd'
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for 'devAskNewPage'
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for 'reshape'
subjplot.OLScurve : plotOLScurve : mypanel: no visible global function
  definition for 'gray'
subjplot.OLScurve: no visible global function definition for
  'devAskNewPage'
Undefined global functions or variables:
  as.formula cor cov devAskNewPage gray lm model.frame model.matrix
  na.omit predict reshape residuals sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "gray")
  importFrom("stats", "as.formula", "cor", "cov", "lm", "model.frame",
             "model.matrix", "na.omit", "predict", "reshape",
             "residuals", "sd")
to your NAMESPACE file.
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'car', 'data.table', 'ggplot2', 'goftest', 'gridExtra', 'nortest',
  'Rcpp'

Packages suggested but not available for checking:
  'covr', 'descriptr', 'knitr', 'rmarkdown', 'testthat', 'vdiffr',
  'xplorerr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
fhcor: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
Packages required but not available:
  'stringr', 'RCurl', 'ggplot2', 'mclust', 'gtools', 'tidyr', 'dplyr',
  'tidyselect', 'pheatmap', 'reshape2', 'plotly', 'knitr', 'rmarkdown',
  'RColorBrewer', 'igraph', 'ggExtra', 'dendextend', 'STRINGdb'

Package suggested but not available for checking: '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:
  'doParallel', 'ROCR', 'irlba', 'foreach'

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:
  'faviconPlease', 'ggplot2', 'opencpu', 'tinytest', 'ttdo', 'UpSetR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'magrittr', 'tibble', 'softImpute'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'gplots'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lme4', 'pheatmap'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'data.table', 'dplyr', 'ff', 'glmnet', 'magrittr',
  'matrixStats', 'purrr', 'rlang', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CompQuadForm', 'stringr', 'survey'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dbplyr', 'dplyr', 'DBI', 'RSQLite'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lazyeval', 'rlang', 'listcomp', 'data.table', 'fastmap'

Packages suggested but not available for checking:
  'covr', 'magrittr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ROI', 'slam', 'ompr'

Packages suggested but not available for checking:
  'testthat', 'magrittr', 'ROI.plugin.glpk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'gt', 'htmltools', 'magrittr', 'rlang', 'sass', 'xml2'

Packages suggested but not available for checking:
  'covr', 'knitr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'dplyr', 'stringr', 'KEGGREST', 'reshape2', 'ggfortify',
  'ggplot2', 'magrittr', 'tidyr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: 'lme4'
Errors in running code in vignettes:
when running code in 'RoeDeerMass-simulation.Rnw'

> library(OnAge)

> data(RoeDeerMassData)

> RoeDeerMassData$ID <- factor(RoeDeerMassData$ID)

> RoeDeerMassData$cohort <- factor(RoeDeerMassData$cohort)

> dataFCH <- RoeDeerMassData[RoeDeerMassData$sex %in% 
+     "F" & RoeDeerMassData$population %in% "CH", ]

> dataMCH <- RoeDeerMassData[RoeDeerMassData$sex %in% 
+     "M" & RoeDeerMassData$population %in% "CH", ]

> dataFTF <- RoeDeerMassData[RoeDeerMassData$sex %in% 
+     "F" & RoeDeerMassData$population %in% "TF", ]

> dataMTF <- RoeDeerMassData[RoeDeerMassData$sex %in% 
+     "M" & RoeDeerMassData$population %in% "TF", ]

> b1 <- function(x, bp) ifelse(x < bp, 0, x - bp)

> ll.real <- function(thr, dataIn) {
+     logLik(lme4::lmer(body.mass ~ b1(age, thr) + age.at.last.capture + 
+         last.year.of.capture + (1 | I .... [TRUNCATED] 

> ll.sim <- function(thr, dataIn) {
+     logLik(lme4::lmer(body.mass.sim ~ b1(age, thr) + age.at.last.capture + 
+         last.year.of.capture + (1  .... [TRUNCATED] 

> search.range <- c(6, 12)

> search.range.TF <- search.range.CH <- search.range

> res.tf <- onset.test(ll.real, dataFTF, dataMTF, search.range.TF, 
+     do.plot = TRUE)

  When sourcing 'RoeDeerMass-simulation.R':
Error: there is no package called 'lme4'
Execution halted

  'RoeDeerMass-simulation.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
--- re-building 'RoeDeerMass-simulation.Rnw' using Sweave

Error: processing vignette 'RoeDeerMass-simulation.Rnw' failed with diagnostics:
 chunk 6 (label = testTF) 
Error in loadNamespace(x) : there is no package called 'lme4'

--- failed re-building 'RoeDeerMass-simulation.Rnw'

SUMMARY: processing the following file failed:
  'RoeDeerMass-simulation.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tibble'

Packages suggested but not available for checking: 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'flextable', 'ggplot2', 'magrittr', 'officer', 'stringr',
  'rlang', 'yaml'

Packages suggested but not available for checking:
  'knitr', 'knitrdata', '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:
  'anytime', 'httr', 'humanize', 'lubridate', 'stringi', 'tictoc',
  'crayon', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'assertthat',
  'checkmate', 'Formula', 'bayesplot', 'ggplot2', 'dplyr', 'tibble',
  'tidyr', 'abind', 'scales', 'rlang', 'tidyselect', 'BH', 'RcppEigen',
  'StanHeaders'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat', 'mvtnorm', 'vdiffr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ade4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ridge', 'car', 'glmnet', 'pls', 'sva', 'preprocessCore',
  'GenomicFeatures', 'genefilter', 'gdata', 'tidyverse', 'readxl',
  'BiocGenerics', 'GenomicRanges', 'IRanges', 'S4Vectors',
  'org.Hs.eg.db', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'maftools'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
generate.data: no visible global function definition for 'rbinom'
least.common.ancestor: no visible global function definition for
  'na.omit'
oncotree.fit : estimate.error.rates: no visible global function
  definition for 'optim'
plot.boottree: no visible global function definition for 'par'
plot.boottree: no visible global function definition for
  'dev.interactive'
plot.boottree: no visible global function definition for 'mtext'
plot.oncotree: no visible global function definition for 'par'
plot.oncotree: no visible global function definition for 'xinch'
plot.oncotree: no visible global function definition for 'yinch'
plot.oncotree: no visible global function definition for 'lines'
plot.oncotree: no visible global function definition for 'rect'
plot.oncotree: no visible global function definition for 'strwidth'
plot.oncotree: no visible global function definition for 'strheight'
plot.oncotree: no visible global function definition for 'text'
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
Packages required but not available:
  'RCurl', 'jsonlite', 'dplyr', 'xgboost', 'pROC', 'ggplot2', 'caret',
  'DALEX', 'rlist', 'readr', 'rlang', 'formattable', 'sparkline',
  'webshot', 'e1071', 'pdp', 'fs', 'scales', 'tidyr', 'htmltools',
  'rjson'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'magrittr', 'rhdf5', 'data.table', 'Rcpp', 'crayon',
  'dplyr', 'Rhdf5lib'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'magrittr'

Packages suggested but not available for checking:
  'genlasso', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'R6', 'glue', 'safer', 'magrittr', 'jsonlite', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'reshape2', 'Rcpp', 'smacof', 'princurve',
  'dplyr', 'tidyr', 'htmlwidgets', 'ggpubr', 'RColorBrewer',
  'dendextend', 'rebus', 'vcfR', 'stringi'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', '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:
  'rlang', 'httr', 'dplyr', 'purrr', 'stringr', 'tidyr', 'future',
  'furrr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'sf', 'rgdal', 'sp'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'jsonlite'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'Formula', 'gmm', 'ivreg', 'lmtest', 'msm'

Packages suggested but not available for checking:
  'AER', 'haven', 'ivtools', 'knitr', 'lfe', '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: 'fitdistrplus', 'numDeriv'

Package suggested but not available for checking: 'actuar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available: 'XML', 'RCurl', 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'moments', 'car', 'ggplot2', 'nortest'

Packages suggested but not available for checking: 'AID', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'emulator'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'VIM'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'R6', 'pbs', 'digest', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'R.rsp', 'testthat', 'data.table', 'plotly'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RSpectra', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 32 marked UTF-8 strings
Package required but not available: 'minpack.lm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'reticulate'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'spatstat.core', 'spatstat.geom', 'spatstat.random'

Packages suggested but not available for checking:
  'covr', 'spatstat', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'readr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'data.table', 'vroom', 'curl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'ontologyIndex', 'visNetwork', 'shinydashboard', 'pbapply',
  'stringr', 'dplyr', 'plyr', 'sunburstR', 'usethis'

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:
  'ontologyIndex', 'paintmap', 'Rgraphviz'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'ontologyIndex'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'paintmap'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mlr', 'randomForest', 'ranger'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'modi'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'keyATM', 'purrr', 'tibble', 'shiny', 'digest', 'R6', 'quanteda',
  'irr', 'ggplot2', 'cowplot', 'cli'

Packages suggested but not available for checking:
  'testthat', 'text2vec', 'BTM', 'dplyr', 'topicmodels', 'stm',
  'seededlda', 'covr', 'stringr', 'knitr', 'rmarkdown', 'fs',
  'quanteda.textmodels', 'shinytest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ci.prop: no visible global function definition for 'qf'
ci.prop: no visible global function definition for 'qnorm'
ePCP: no visible global function definition for 'qnorm'
sevennum: no visible global function definition for 'na.omit'
sevennum: no visible global function definition for 'quantile'
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
Package required but not available: 'R6'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'withr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Packages required but not available:
  'caret', 'dplyr', 'forecast', 'furrr', 'future', 'ggplot2', 'glmnet',
  'imputeTS', 'lmtest', 'lubridate', 'magrittr', 'purrr', 'sandwich',
  'tidyr', 'vars', 'xts', 'zoo'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'quantmod'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'mime', 'progress', 'labelled'

Packages suggested but not available for checking:
  'e1071', 'knitr', 'knitrBootstrap', 'rmarkdown', 'tibble', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'assertthat', 'combinat', 'ggplot2'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rjson', 'RCurl', 'reshape2', 'triangle', 'httpRequest', 'digest',
  'xtable', 'ggplot2', 'rgdal', 'sp', 'plyr', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caTools', 'pracma', 'twosamples', 'benchmarkme', 'memuse',
  'doParallel', 'foreach'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gmp', 'mvtnorm', 'orthopolynom', 'crossdes', 'polynom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'jsonlite', 'readr', 'dplyr', 'tibble', 'xml2', 'maptools',
  'rappdirs'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'leaflet', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlang', 'dplyr', 'purrr', 'tidyr', 'readr', 'latticeExtra',
  'lubridate', 'mapproj', 'hexbin', 'Rcpp'

Packages suggested but not available for checking:
  'maps', 'mapdata', 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'httpcode', 'jsonlite', 'dplyr', 'magrittr', 'tidyr', 'glue'

Packages suggested but not available for checking:
  'testthat', 'lintr', '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: 'httr', 'jsonlite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'dplyr', 'lifecycle', 'jsonlite', 'memoise', 'progress',
  'purrr', 'ratelimitr', 'rlang', 'tibble', 'tidyr', 'withr'

Packages suggested but not available for checking:
  'knitr', 'mockery', 'rmarkdown', 'sf', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/r_packages/pkgcheck/CRAN/OpenCL/OpenCL.Rcheck/00install.out' for details.
Packages required but not available:
  'evaluate', 'httpuv', 'knitr', 'jsonlite', 'remotes', 'sys',
  'webutils', 'curl', 'rappdirs', 'zip', 'mime', 'protolite', 'brew',
  'openssl'

Packages suggested but not available for checking:
  'arrow', 'unix', 'haven', 'pander', 'R.rsp', 'svglite'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'secr', 'Rcpp', 'stringr', 'plyr', 'abind', 'RcppParallel', 'BH'

Packages suggested but not available for checking:
  'knitr', 'RMark', 'rgdal', 'R2ucare', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ckanr', 'magrittr', 'readxl', 'sf', 'tibble', 'xml2', 'curl'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'knitr', 'purrr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'ggplot2'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
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  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'airports', 'cherryblossom', 'usdata', 'ggplot2', 'readr',
  'rmarkdown', 'tibble'

Packages suggested but not available for checking:
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  'testthat', 'tidyr', 'tidytext'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'gridExtra', 'circlize', 'networkD3',
  'raster'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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Packages suggested but not available for checking:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'BBmisc', 'checkmate', 'data.table', 'digest', 'httr',
  'stringi', 'XML', 'jsonlite', 'memoise', 'curl'

Packages suggested but not available for checking:
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  'farff', 'knitr', 'rmarkdown', 'R.rsp', 'lintr', 'rex'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'digest', 'Rcpp', 'RcppParallel', 'lifecycle', 'RcppEigen',
  'StanHeaders', 'BH', 'rpf'

Packages suggested but not available for checking:
  'mvtnorm', 'numDeriv', 'roxygen2', 'rpf', 'snowfall', 'lme4', 'covr',
  'testthat', 'umx', 'ifaTools', 'knitr', 'markdown', 'rmarkdown',
  'reshape2', '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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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'NLP', 'openNLPdata', 'rJava'

Package suggested but not available for checking: 'openNLPmodels.en'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'shinydashboard', 'shinydashboardPlus', 'shinycssloaders',
  'shinyFeedback', 'rintrojs', 'formattable', 'openxlsx', 'DT',
  'magrittr', 'tidyverse', 'dplyr', 'stringr', 'reshape2', 'scales',
  'igraph', 'testthat', 'tidyr', 'withr', 'RColorBrewer'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'stringr', 'abind', 'rgl', 'colorspace', 'GPArotation',
  'psych', 'XML', 'pvclust', 'openxlsx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'ssh', 'xml2', 'ggmap', 'ggplot2', 'magick', 'R6', 'dbscan'

Packages suggested but not available for checking:
  'knitr', 'BiocStyle', 'RUnit', 'BiocGenerics', 'rmarkdown',
  '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', 'rlang', 'osfr', 'hyperSpec', 'hexView', 'digest', 'signal',
  'shiny'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'config', 'shinyjs', 'shinythemes',
  'shinyBS', 'shinyWidgets', 'ggplot2', 'plotly', 'data.table', 'DT',
  'curl', 'rdrop2', 'mongolite', 'loggit'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'askpass'

Packages suggested but not available for checking:
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  'jose', 'sodium'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'rgrass7', 'progress', 'rgdal', 'sp', 'raster', 'SSN'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'rJava', 'raster', 'rgdal', 'sp'

Packages suggested but not available for checking: 'colorspace', 'maptools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'DBI', 'RSQLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'maptools', 'openair', 'raster', 'rgdal', 'reshape',
  'doParallel', 'foreach', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'geodist', 'googlePolylines', 'curl',
  'rjson', 'pbapply', 'lubridate', 'sf', 'sfheaders'

Packages suggested but not available for checking:
  'RcppSimdJson', 'covr', 'knitr', 'rmarkdown', 'testthat', 'raster',
  'rgdal', '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:
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  'cli'

Packages suggested but not available for checking: 'nbc4va', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'stringi', 'zip'

Packages suggested but not available for checking:
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VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'Rdpack', 'RcppEigen'

Packages suggested but not available for checking:
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  'gbm', 'rmarkdown', 'magrittr'

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 suggested but not available for checking:
  'operators', 'magrittr', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'AdaptGauss', 'DataVisualizations', 'DistributionOptimization',
  'mixtools', 'foreach', 'rlang', 'ggplot2', 'caTools', 'dplyr',
  'mclust', 'mixAK', 'multimode', 'NbClust', 'ClusterR', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tibble', 'tidytext', 'magrittr', 'dplyr', 'stringr',
  'purrr', 'tidyr', 'likert', 'tm', 'wordcloud2', 'forcats', 'cowplot'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'rvest', 'kableExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'hopbyhop', 'endtoend'
Packages required but not available:
  'magrittr', 'uuid', 'proto', 'cli', 'assertthat', 'tibble', 'ape',
  'tidytree', 'ggplot2', 'viridisLite', 'lpSolveAPI', 'withr', 'Rcpp',
  'RcppArmadillo', 'RcppProgress'

Packages suggested but not available for checking:
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  'Rsymphony', 'lpsymphony', 'shiny', 'rhandsontable', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'matrixcalc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nlsolve: no visible global function definition for 'optim'
nlsolve: no visible global function definition for 'runif'
optAUC: no visible global function definition for 'var'
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rpanel', 'randomForest', 'e1071', 'ipred', 'msm', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Ckmeans.1d.dp', 'plotrix', 'Rcpp', 'Rdpack', 'reshape2'

Packages suggested but not available for checking:
  'ape', 'ggplot2', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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Packages suggested but not available for checking:
  'Biobase', 'GO.db', 'org.At.tair.db', 'annotate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'purrr', 'rlang', 'crayon', 'cli', 'magrittr', 'dplyr',
  'nleqslv', 'shiny', 'DT', 'shinydashboard', 'shinyalert', 'plotly',
  'hrbrthemes', 'shinyjs', 'orthopolynom'

Packages suggested but not available for checking:
  'testthat', 'mockery', 'markdown', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Packages required but not available:
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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: 'ggplot2', 'magrittr'

Packages suggested but not available for checking:
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  'knitr', 'plyr', 'reshape2', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pbapply', 'pscl', 'betareg', 'ResourceSelection', 'mefa4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringi', 'magrittr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lpSolve', 'matrixStats', 'matrixcalc', 'plyr', 'quadprog', 'rgl'

Packages which this enhances but not available for checking:
  'gurobi', 'slam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'glue', 'magrittr', 'rlang', 'tibble'

Packages suggested but not available for checking:
  'bslib', 'DiagrammeR', 'DT', 'globals', 'knitr', 'rmarkdown',
  'shiny', 'shinytest', 'survey', 'testthat', '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:
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ars', 'rjags', 'HDInterval', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mstate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DepthProc', 'fields', 'geometry', 'magrittr', 'mclust', 'nloptr',
  'rsm', 'Rdpack', 'Rdsdp', 'spam', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'lhs', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Skipping vignette re-building
Packages suggested but not available for checking:
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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: 'lhs', 'randtoolbox', 'stringr'

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: 'ucminf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'colorspace'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lpSolveAPI', 'tidyr', 'dplyr'

Packages suggested but not available for checking: 'readxl', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tidyverse', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
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  'numDeriv', 'lbfgsb3c'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'optextras', 'numDeriv', 'setRNG', 'Rvmmin', 'Rcgmin'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'optimbase'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder 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', 'mvtnorm', 'cubature'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvabund', 'ordinal'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'setRNG', 'BB', 'ucminf', 'minqa', 'dfoptim',
  'lbfgsb3c', 'lbfgs', 'subplex'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'clinfun'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rootSolve', 'distances', 'weights', 'pbapply', 'Hmisc'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'magrittr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'data.table', 'ggplot2', 'AUC', 'knitr', 'plyr', 'scales', 'stringr',
  'XML'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plyr', 'kinship2', 'nadiv', 'pedigree', 'pspline', 'stringr',
  'purrr', 'quadprog', 'data.table', 'magic', 'doParallel', 'foreach',
  'ECOSolveR', 'reshape2', 'optiSolve', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shapes', 'alabama', 'cccp', 'nloptr', 'plyr', 'stringr', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'tidyverse', 'shiny',
  'shinydashboard'

VignetteBuilder package required for checking but not installed: 'knitr'
Package unavailable to check Rd xrefs: 'tibble'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'rlemon', 'survey'

Packages suggested but not available for checking:
  'RItools', 'biglm', 'testthat', 'roxygen2', 'brglm', 'arm', 'knitr',
  'rmarkdown', 'markdown', 'pander', 'xtable', 'rrelaxiv'

Packages which this enhances but not available for checking:
  'CBPS', 'haven'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'SiZer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'getopt'

Packages suggested but not available for checking:
  'knitr', 'stringr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'labdsv', 'plotrix'

Package suggested but not available for checking: 'tree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pwr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'osqp', 'ggplot2'

Packages suggested but not available for checking: 'cobalt', 'twang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'arules'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'VineCopula', 'tea', 'actuar', 'truncnorm', 'ReIns', 'pracma',
  'evmix'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DBI', 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'graph'
Packages required but not available: 'BiasedUrn', 'BlakerCI', 'PropCIs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Iso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'bookdown', 'knitr', 'latticeExtra', 'plotrix', 'Rcpp',
  'remotes', 'rgdal', 'sf', 'sp'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lmtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'faux', 'dplyr', 'brms', 'tidyr'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'ggplot2', 'modelsummary', 'marginaleffects',
  'haven', 'stringr', '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: 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'distances', 'Rfast', 'plyr', 'foreach', 'doRNG', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls to packages already attached by Depends:
  'Matrix' 'splines'
  Please remove these calls from your code.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for 'ecdf'
bgmm : SplineGMM: no visible global function definition for
  'constrOptim'
blr: no visible global function definition for 'ecdf'
blr: no visible global function definition for 'constrOptim'
blr: no visible global function definition for 'lm'
parentcdf : combinations: no visible global function definition for
  'combn'
parentcdf : solver: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package required but not available: 'hash'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'na.tools'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'DBI', 'R6', 'RSQLite', 'crayon', 'digest', 'docopt', 'fs', 'gert',
  'ids', 'withr', 'yaml', 'zip'

Packages suggested but not available for checking:
  'httr', 'jsonlite', 'knitr', 'markdown', 'mockery', 'processx',
  'rmarkdown', 'testthat', 'vaultr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Newdistns', 'gamlss.dist', 'actuar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'eha'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'coda', 'devtools', 'dclone', 'runjags', 'DESeq2',
  'SummarizedExperiment'

Packages suggested but not available for checking:
  'knitr', 'Biobase', '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:
  'Rcpp', 'RcppProgress', 'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'caret', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Deriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'combinat', 'verification'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'VGAM'
Packages required but not available: 'reshape2', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mirt', 'NominalLogisticBiplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'glmnet', 'penalized', 'VGAM', 'rms'
Packages required but not available: 'gtools', 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ucminf', 'numDeriv'

Packages suggested but not available for checking:
  'lme4', 'xtable', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rjags'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'corpcor', 'GenOrd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'grplasso', 'RLRsim', 'quadprog', 'glmpath'

Packages suggested but not available for checking:
  'psy', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'gridExtra', 'ggplot2', 'openxlsx', 'spectral', 'pracma',
  'fftwtools', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'crayon', 'rex', 'tinytest', 'covr'
Found the following sources/headers with CR or CRLF line endings:
  src/onig/config.h
Some Unix compilers require LF line endings.
Package required but not available: 'httr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ranger', 'Rcpp', 'xtable'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggthemes', 'ggplot2', 'lubridate', 'data.table', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'textutils'

Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ORICC1: no visible binding for global variable 'sd'
ORICC1: no visible global function definition for 'write.table'
ORICC1: no visible global function definition for 'postscript'
ORICC1: no visible global function definition for 'jpeg'
ORICC1: no visible global function definition for 'points'
ORICC1: no visible global function definition for 'dev.off'
ORICC1: no visible global function definition for 'par'
ORICC2: no visible binding for global variable 'sd'
ORICC2: no visible global function definition for 'write.table'
ORICC2: no visible global function definition for 'postscript'
ORICC2: no visible global function definition for 'jpeg'
ORICC2: no visible global function definition for 'points'
ORICC2: no visible global function definition for 'dev.off'
ORICC2: no visible global function definition for 'par'
Undefined global functions or variables:
  dev.off jpeg par points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages suggested but not available for checking: 'rgl', 'scatterplot3d'
Packages unavailable to check Rd xrefs: 'rgl', 'scatterplot3d'
Running examples in 'orientlib-Ex.R' failed
The error most likely occurred in:

> ### Name: boat3d
> ### Title: Draw boat glyphs for orientation data
> ### Aliases: boat3d
> ### Keywords: hplot dynamic
> 
> ### ** Examples
> 
> x <- eulerzyx(psi=c(0,pi/4,0,0), theta=c(0,0,pi/4,0), phi=c(0,0,0,pi/4))
> 
> # Need a 3D renderer; assume scatterplot3d, but others could be used
> 
> s <- boat3d(x, 0:3, axes = FALSE, graphics = 'scatterplot3d')
Error in boat3d(x, 0:3, axes = FALSE, graphics = "scatterplot3d") : 
  Need 3D renderer:  rgl or scatterplot3d
Execution halted
Packages required but not available:
  'abind', 'data.table', 'assertthat', 'future', 'future.apply',
  'listenv'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'knitr', 'stringr', 'glmnet', 'forecast',
  'randomForest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rstudioapi'

Packages suggested but not available for checking:
  'data.table', 'dplyr', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TunePareto', 'e1071', 'knitr', 'rmarkdown', 'doParallel', 'igraph',
  'foreach', 'randomForest'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package 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: 'orloca'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'png', 'ucminf', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rms', 'Hmisc', 'doParallel', 'foreach', 'iterators', 'SparseM',
  'benchmarkme'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
mdr.c: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages required but not available: 'ggplot2', 'rms', 'gtable'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'knitr', 'rmarkdown', 'pander'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'oro.nifti'

Packages suggested but not available for checking: 'testthat', 'hwriter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bitops', 'abind', 'RNifti'

Packages suggested but not available for checking:
  'XML', 'testthat', 'covr', 'knitr', 'rmarkdown', 'rticles'

Packages which this enhances but not available for checking:
  'fmri', 'oro.dicom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'oro.dicom', 'oro.nifti', 'minpack.lm', 'msm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'gtools', 'genefilter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sp'

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: 'BB', 'BHH2'

Package suggested but not available for checking: 'setRNG'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'dr', 'pracma', 'plot3D', 'rgl', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plot.SplineBasis: no visible global function definition for 'matplot'
plot,SplineBasis-matrix: no visible global function definition for
  'matplot'
plot,SplineBasis-missing: no visible global function definition for
  'matplot'
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'polynom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'googleAuthR', 'googleCloudVisionR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'stringr', 'tm', 'tibble', 'tidytext', 'topicmodels',
  'rmarkdown', 'xlsx', 'knitr'

Packages suggested but not available for checking: 'reshape2', 'qpdf'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'raster'

Packages suggested but not available for checking: 'testthat', 'maps'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mc2d'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'JADE', 'nnls'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'jsonlite', 'stringi', 'purrr', 'tibble', 'rlang', 'fs',
  'memoise', 'httr'

Packages suggested but not available for checking:
  'dplyr', 'logger', 'rprojroot', 'testthat', 'knitr', 'rmarkdown',
  'lintr', 'covr', 'spelling'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'unitizer', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'run.R'
Running the tests in 'tests/run.R' failed.
Complete output:
  > library(unitizer)
  Error in library(unitizer) : there is no package called 'unitizer'
  Execution halted
Packages suggested but not available for checking:
  'askpass', 'testthat', 'withr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'XML', 'RCurl', 'geosphere'

Packages suggested but not available for checking: 'igraph', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'curl', 'httr', 'jsonlite', 'lubridate', 'magrittr', 'Rcpp',
  'reproj', 'rvest', 'sp', 'tibble', 'xml2'

Packages suggested but not available for checking:
  'knitr', 'markdown', 'raster', 'rmarkdown', 'sf', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'geoR', 'mapview', 'nngeo', 'osmdata', 'pdist', 'processx',
  'rgdal', 'sp', 'splancs', 'qpdf', 'Rcpp', 'tibble', 'sf'

Packages suggested but not available for checking:
  'PrevMap', 'rmarkdown', 'markdown', 'leafem', 'viridisLite',
  'raster', 'knitr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rlist', 'knitr', 'rmarkdown', 'stringr', 'ncdf4', 'fields'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'e1071', 'ggm', 'ggplot2', 'mapproj', 'osmdata', 'rgeos', 'sp',
  'spatstat', 'spatstat.core', 'spatstat.geom'

Packages suggested but not available for checking:
  'curl', 'knitr', 'magrittr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'OpenStreetMap', 'berryFunctions', 'sp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'R6'

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: 'Rcpp', 'R6'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'jsonlite', 'curl', 'isoband', 'googlePolylines', 'sf'

Packages suggested but not available for checking:
  'mapsf', 'lwgeom', 'tinytest', 'covr', 'sp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'assertthat', 'bitops', 'rjson', 'R.utils', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'microbenchmark'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sfsmisc', 'matrixStats', 'circular', 'hypervolume', 'ggplot2',
  'gridExtra', 'viridis'

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', 'pec', 'prodlim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rglpk', 'sm', 'transport'

Package suggested but not available for checking: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'base64url', 'openssl'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'httr', 'geojsonsf', 'janitor', 'jsonlite', 'sf',
  'urltools', 'dplyr', 'rrapply', 'rlang'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'mice', 'missMDA', 'plyr', 'FactoMineR', 'StatMatch',
  'proxy', 'rdist', 'ROI', 'ROI.plugin.glpk', 'ompr', 'ompr.roi',
  'party', 'vcd'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'foreach', 'doParallel', 'robustbase', 'mclust'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'sigmoid', 'reticulate'

Packages suggested but not available for checking:
  'testthat', 'stream', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/otsad.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'httr', 'fs', 'rmarkdown', 'xml2', 'rvest', 'readr',
  'R.utils', 'bookdown', 'glue', 'curl', 'rprojroot', 'magrittr',
  'yaml', 'stringr', 'knitr', 'purrr'

Packages suggested but not available for checking:
  'remotes', '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:
  'yaml', 'testthat', 'jsonlite', 'pryr', 'R6', 'zip'

Package suggested but not available for checking: 'IRdisplay'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'vegan', 'reshape2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'ggplot2', 'gridExtra', 'Hmisc', 'moments', 'quantreg',
  'scales', 'stringi'

Packages suggested but not available for checking:
  'bit64', 'knitr', 'proto', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'subplex'

Packages suggested but not available for checking: 'ape', 'geiger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ape', 'ggplot2', 'magrittr', 'visNetwork'

Packages suggested but not available for checking:
  'coda', 'microbenchmark', 'testthat', 'knitr', 'rmarkdown', 'igraph',
  'epicontacts'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'covr', 'ape', 'incidence'
Running examples in 'outbreaks-Ex.R' failed
The error most likely occurred in:

> ### Name: nipah_malaysia
> ### Title: Nipah in Malaysia and Sinagapore, 1997-1999
> ### Aliases: nipah_malaysia
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## show first few weeks of Dengue incidence
> head(nipah_malaysia)
        date perak negeri_sembilan selangor singapore
1 1997-01-04     0               0        0         0
2 1997-01-11     1               0        0         0
3 1997-01-18     0               0        0         0
4 1997-01-25     1               0        0         0
5 1997-02-01     1               0        0         0
6 1997-02-08     0               0        0         0
> 
> ## convert data to incidence object and plot epicurve using the incidence package
> library(incidence)
Error in library(incidence) : there is no package called 'incidence'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'Rdpack'

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggplot2', 'knitr', 'testthat', 'tidyr', 'covr',
  'rmarkdown', 'spelling', 'stringr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ranger', 'FNN', 'missRanger'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', '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:
  'quantreg', 'MatrixModels', 'outliers', 'pcaPP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'airt', 'EstCRM', 'psych', 'apcluster'

Packages suggested but not available for checking:
  'DDoutlier', '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:
  'rlist', 'ggplot2', 'dplyr', 'tidyr', 'forcats', 'HDoutliers',
  'robustbase', 'robustX', 'FastPCS', 'cellWise', 'GGally', 'memisc'

Packages suggested but not available for checking:
  'knitr', 'gridExtra', 'rmarkdown', 'languageR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'Rcereal'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'kableExtra', 'magrittr', '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: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'reshape2', 'sandwich', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'AER', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crayon', 'devtools', 'pkgload', 'sys', 'yaml', 'callr', 'tibble',
  'cli'

Packages suggested but not available for checking: 'ssh', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'outsider.base', 'remotes', 'crayon', 'jsonlite', 'tibble', 'curl',
  'yaml'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'ape', 'rlang', 'ssh'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'corpcor', 'nloptr', 'geiger', 'RColorBrewer', 'igraph',
  'numDeriv', 'phytools', 'paleotree', 'phangorn', 'lhs', 'interp',
  'phylolm'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'coda', 'Sim.DiffProc', 'MCMCpack', 'abc', 'phytools',
  'TreeSim', 'adephylo', 'maps', 'geiger', 'EasyABC'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'spatstat.geom'

Packages suggested but not available for checking: 'maptools', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'maptools', 'sp'
Package required but not available: 'bigmemory'

Packages suggested but not available for checking:
  'testthat', 'mockery', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'covr', 'devtools', 'knitr', 'pkgdown', 'rmarkdown', 'spelling',
  'testthat'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'twang', 'Amelia', 'EnvStats', 'devtools', 'dplyr', 'ggplot2',
  'ggrepel', 'glue', 'magrittr', 'metR', 'purrr', 'progress', 'rlang',
  'survey', 'tibble', 'tidyselect', 'varhandle'

Packages suggested but not available for checking: 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'dplyr', 'httr', 'jsonlite', 'data.table', 'magrittr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tinytest'
Packages required but not available: 'gtools', 'shiny'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'BH', 'RcppNumerical', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'mvtnorm'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'rvest', 'readr', 'leaflet', 'stringr', 'ggplot2', 'sf',
  'magrittr', 'forcats', 'jsonlite', 'htmltools', 'purrr', 'xml2',
  'curl', 'ggrepel', 'scales', 'rlang', 'httr'

Packages suggested but not available for checking:
  'testthat', 'showtext', 'sysfonts', 'knitr', 'rmarkdown', 'plm',
  'texreg'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'httr', 'jsonlite', 'plyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'leaflet', 'whisker', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'geometa', 'keyring', 'R6', 'httr', 'openssl', 'XML', 'sf', 'rgdal'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stringi', 'stringr', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown', 'ggplot2', 'ggridges'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'checkmate', 'dplyr', 'magrittr', '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(ox)
  > testthat::test_check("ox")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'cli', 'dplyr', 'glue', 'httr', 'jsonlite', 'purrr', 'rjson',
  'rlang', 'stringr', 'tibble', 'tidyr', 'yaml'

Packages suggested but not available for checking:
  'covr', 'httptest', 'knitr', 'rmarkdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'oz', 'tibble', 'sf'

Packages suggested but not available for checking:
  'paletteer', 'testthat', 'covr', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
loadCSVtoP2distance: no visible global function definition for
  'read.table'
p2distance : calcularDistancia: no visible binding for global variable
  'sd'
p2distance : ordenarVariables: no visible global function definition
  for 'cor'
p2distance : calculoFactoresPonderacion: no visible global function
  definition for 'lm'
p2distance: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'terms'
p3state: no visible global function definition for 'as.formula'
p3state: no visible global function definition for 'coxph'
p3state: no visible binding for global variable 'na.exclude'
plot.p3state: no visible global function definition for 'matplot'
plot.p3state: no visible global function definition for 'devAskNewPage'
plot.p3state: no visible global function definition for 'persp'
plot.p3state: no visible global function definition for 'colours'
plot.p3state: no visible global function definition for
  'filled.contour'
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
pacbpred : thetaFunc: no visible global function definition for 'lsfit'
pacbpred : thetaFunc: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'var'
pacbpred: no visible global function definition for 'runif'
pacbpred: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Packages required but not available: 'diffr', 'htmlwidgets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'pander', 'formattable', 'stringr', 'crayon',
  'lubridate', 'tidyr', 'textutils', 'htmlTable', 'clipr', 'shiny',
  'reactable', 'shinyjs', 'shinybusy', 'rstudioapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cranlogs', 'data.table', 'ggplot2', 'memoise', 'pkgsearch', 'RCurl',
  'R.utils', 'rversions', 'sugrrants'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'callr', 'checkmate', 'crayon', 'cyclocomp', 'desc', 'fakemake',
  'fritools', 'fs', 'gert', 'httr', 'pkgbuild', 'pkgload', 'rcmdcheck',
  'remotes', 'rhub', 'rprojroot', 'tinytest', 'whisker', 'whoami'

Packages suggested but not available for checking:
  'cleanr', 'covr', 'devtools', 'digest', 'document', 'knitr', 'lintr',
  'rasciidoc', 'rmarkdown', 'roxygen2', 'RUnit', 'spelling',
  'testthat', 'usethis', 'withr'

VignetteBuilder package required for checking but not installed: 'rasciidoc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'rappdirs', 'httr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Packages suggested but not available for checking:
  'ggiraph', 'ggplot2', 'knitr', 'rmarkdown', 'lpSolve'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readxl', 'stringr', 'data.table', 'reshape2', 'rlang', 'lme4',
  'flexsurv', 'survminer', 'SurvRegCensCov', 'systemfit',
  'IPDFileCheck', 'valueEQ5D', 'car', 'ggplot2', 'lmtest', 'broom',
  'effects', 'gvlma', 'relaimpo', 'tm', 'tidyverse', 'tibble', 'dplyr',
  'tidyr', 'hash', 'haven'

Packages suggested but not available for checking:
  'ISLR', 'knitr', 'rmarkdown', 'covr', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fs', 'usethis', 'jsonlite', 'htmlwidgets', 'cli', 'assertthat',
  'rprojroot', 'rstudioapi'

Packages suggested but not available for checking:
  'testthat', 'covr', 'golem'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'WriteXLS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ade4', 'pROC', 'DiscriMiner', 'doParallel', 'foreach', 'FactoMineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', 'httr', 'knitr', 'rmarkdown'
Running 'test-cranlike-repositories.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
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW: warning in return(x@u1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@u2): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@w1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW: warning in x@u1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@u2 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@w1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
Unknown package 'packClassic' in Rd xrefs
Packages required but not available:
  'penalized', 'lars', 'quadprog', 'limSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'remotes'

Packages suggested but not available for checking:
  'BiocManager', 'knitr', 'testthat', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'vegan', 'ape', 'plyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'VineCopula', 'numDeriv', 'ggplot2', 'gridExtra',
  'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'igraph', 'parmigene', 'infotheo', 'dplyr', 'Rtsne',
  'ggplot2', 'ggrepel'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'memoise', 'stringi', 'xml2', 'renv', 'jsonlite', 'curl'

Packages suggested but not available for checking:
  'remotes', 'withr', 'pkgsearch', 'mockery', 'testthat', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'circlize', 'e1071', 'plotrix'

Packages suggested but not available for checking: 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RCircos', 'optparse', 'genbankr', 'BiocGenerics', 'Biostrings',
  'GenomicAlignments', 'GenomicRanges', 'IRanges'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'covr', 'tinytest'
Packages required but not available: 'Rcpp', 'dplyr', 'lubridate', 'rlang'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'knitr', 'rmarkdown', 'lazyeval', 'tidyr',
  'data.table'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'exams', 'stringr', 'curl'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RColorBrewer', 'VGAM', 'magicaxis', 'networkDynamic',
  'network', 'plyr', 'igraph', 'mapproj', 'knitr', 'ggplot2'

Package suggested but not available for checking: 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
paf: no visible global function definition for 'as.formula'
paf: no visible global function definition for 'model.response'
paf: no visible global function definition for 'model.frame'
paf: no visible global function definition for 'model.matrix'
plot.paf: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'stringr', 'rlang'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'ggpubr', 'rmarkdown', 'microbenchmark'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rmarkdown', 'bookdown', 'htmltools', 'jsonlite', 'later',
  'processx', 'servr', 'httpuv', 'xfun', 'websocket'

Packages suggested but not available for checking:
  'promises', 'testit', 'xaringan', 'pdftools', 'revealjs', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'htmlwidgets'

Packages suggested but not available for checking:
  'knitr', 'shiny', 'rmarkdown', 'devtools'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggplot2', 'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'pagenum-Ex.R' failed
The error most likely occurred in:

> ### Name: pagenum
> ### Title: Put Page Numbers on Graphics
> ### Aliases: pagenum setPagenum getPagenum
> 
> ### ** Examples
> 
> # base graphics
> setPagenum(1)
> plot(Sepal.Length~Sepal.Width, data=iris, col=Species, pch=19)
> pagenum()
> 
> # lattice, date
> setPagenum(getPagenum()+1) # Manual increment
> require(lattice)
Loading required package: lattice
> xyplot(Sepal.Length~Sepal.Width, data=iris, groups=Species)
> pagenum(date=TRUE)
> 
> # ggplot2, top-right
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
> ggplot(iris, aes(x=Sepal.Width, y=Sepal.Length,
+   color=Species)) + geom_point() + theme_classic()
Error in ggplot(iris, aes(x = Sepal.Width, y = Sepal.Length, color = Species)) : 
  could not find function "ggplot"
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'jsonlite', 'httr', 'curl'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'WikipediR', 'WikidataR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'igraph', 'dendsort', 'drat', 'fastcluster', 'irlba', 'magrittr',
  'N2R', 'plyr', 'R.utils', 'Rcpp', 'rjson', 'rlang', 'R6', 'RMTstat',
  'Rook', 'Rtsne', 'sccore', 'urltools', 'RcppArmadillo',
  'RcppProgress', 'RcppEigen'

Packages suggested but not available for checking:
  'AnnotationDbi', 'base64enc', 'BiocGenerics', 'BiocParallel',
  'colorRamps', 'data.table', 'dbscan', 'dplyr', 'ggplot2', 'GO.db',
  'gridExtra', 'knitr', 'org.Dr.eg.db', 'org.Hs.eg.db', 'org.Mm.eg.db',
  'pcaMethods', 'pheatmap', 'rgl', 'rmarkdown', 'robustbase', 'scde',
  'testthat', 'uwot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'S4Vectors', 'Biostrings', 'ggplot2', 'R6', 'reshape2', 'vegan',
  'GenomicRanges', 'BiocGenerics', 'shinyWidgets', 'shinydashboard',
  'DT', 'plotly', 'magrittr', 'heatmaply', 'dendextend', 'ggfortify',
  'shiny'

Packages suggested but not available for checking:
  'micropan', 'patchwork', 'ape', 'phangorn', 'pegas', 'DECIPHER',
  'rhierbaps', 'IRanges', 'knitr', 'rmarkdown', 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lars', 'foreach', 'mnormt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'knitr', 'patchwork', 'spelling', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
paired.Loc: no visible global function definition for 'qt'
paired.Loc: no visible global function definition for 'median'
paired.Loc: no visible global function definition for 'qsignrank'
paired.Loc: no visible global function definition for 'qnorm'
paired.Scale: no visible global function definition for 'var'
paired.Scale: no visible global function definition for 'cor'
paired.Scale: no visible global function definition for 'qt'
paired.Scale: no visible global function definition for 'median'
paired.Scale: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
Packages required but not available: 'gld', 'mvtnorm', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'htmlwidgets', 'shiny'

Package suggested but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'TSP', 'gtools', 'graph'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Sleuth3', 'colorspace', 'multcomp', 'igraph',
  'scales', 'RColorBrewer', 'alr4', 'scagnostics'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'MCPAN', 'coin', 'mcprofile'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'psych'
Packages required but not available: 'dplyr', 'magrittr'

Packages suggested but not available for checking: 'R.rsp', 'testthat'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'callr', 'cli', 'covr', 'curl', 'distro', 'filelock', 'glue',
  'mockery', 'pingr', 'jsonlite', 'pkgcache', 'pkgdepends',
  'pkgsearch', 'prettyunits', 'processx', 'ps', 'rprojroot',
  'rstudioapi', 'testthat', 'tibble', 'withr'
Packages unavailable to check Rd xrefs: 'pkgdepends', 'distro', 'pkgsearch'
Packages required but not available:
  'TeachingDemos', 'rioja', 'tibble', 'dplyr', 'magrittr', 'ggplot2',
  'forcats', 'assertr', 'vegan', 'rlang', 'ggrepel', 'tidyr', 'purrr'

Packages suggested but not available for checking:
  'fields', 'knitr', 'rmarkdown', 'gstat', 'sp', 'tidyverse'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'glmnet'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

Packages which this enhances but not available for checking:
  'ashr', 'CorShrink', 'pROC', 'edgeR'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'maps', 'rjson', 'gtools', 'RCurl', 'plyr', 'scales'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ape', 'fitdistrplus', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'paleobuddy-Ex.R' failed
The error most likely occurred in:

> ### Name: find.lineages
> ### Title: Separate a paleobuddy simulation into monophyletic clades
> ### Aliases: find.lineages
> 
> ### ** Examples
> 
> ###
> # first, we run a simple simulation with one starting species
> 
> # set seed
> set.seed(1)
> 
> # run simulation with a minimum of 20 species
> sim <- bd.sim(n0 = 3, lambda = 0.1, mu = 0.1, tMax = 10, 
+               nFinal = c(20, Inf))
> 
> # get a simulation object with the clade originating from species 2
> clades <- find.lineages(sim, S = 2)
> 
> # now we can check to make sure the subclade was correctly separated
> 
> # change NA to 0 on the clade's TE
> clades[[1]]$sim$TE[clades[[1]]$sim$EXTANT] <- 0
> 
> # plot the phylogeny
> if (requireNamespace("ape", quietly = TRUE)) {
+   plot <- ape::plot.phylo(
+     make.phylo(clades[[1]]$sim),
+     main = "red: extinction events \n blue: speciation events");
+   ape::axisPhylo()
+ }
> 
> # check speciation times
> for (j in 2:length(clades[[1]]$sim$TS)) {
+   # the subtraction is just to adjust the wt with the plot scale
+   lines(x = c(
+     sort(clades[[1]]$sim$TS, decreasing = TRUE)[2] -
+        clades[[1]]$sim$TS[j],
+     sort(clades[[1]]$sim$TS, decreasing = TRUE)[2] -
+        clades[[1]]$sim$TS[j]),
+     y = c(plot$y.lim[1], plot$y.lim[2]), lwd = 2, col = "blue")
+ }
Error: object of type 'closure' is not subsettable
Execution halted
Packages required but not available:
  'GCD', 'locfit', 'raster', 'ggplot2', 'plyr', 'rgdal'

Packages suggested but not available for checking:
  'gtools', 'caTools', 'pscl', 'agricolae', 'Imap', 'sp', 'rworldmap',
  'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vegan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'knitr', 'testthat', 'abind', 'rgl'
Package unavailable to check Rd xrefs: 'rgl'
'LazyData' is specified without a 'data' directory
Running examples in 'paleomorph-Ex.R' failed
The error most likely occurred in:

> ### Name: plotSpecimens
> ### Title: Plot an array of specimen landmark data in an interactive 3D
> ###   frame
> ### Aliases: plotSpecimens
> 
> ### ** Examples
> 
> A <- array(rep(rnorm(3 * 20, sd = 30), by = 6) + rnorm(6 * 20 * 3), 
+        dim = c(20, 3, 6))
> plotSpecimens(A)
Error: Package rgl needed for this function to work. Please install it with install.packages('rgl').
Execution halted
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'poems', 'R6', 'sf'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'markdown', 'dplyr', 'raster'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'phangorn', 'phytools', 'jsonlite', 'png', 'RCurl'

Packages suggested but not available for checking: 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mnormt', 'foreach', 'iterators', 'doParallel'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'prismatic', 'rematch2', 'rlang', 'rstudioapi'

Packages suggested but not available for checking:
  'covr', 'gameofthrones', 'ggplot2', 'ggthemes', 'harrypotter',
  'knitr', 'oompaBase', 'palr', 'pals', 'rmarkdown', 'scico',
  'testthat', 'vdiffr', 'viridisLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'knitr', 'rmarkdown'
Packages suggested but not available for checking: 'ggplot2', 'magrittr'
Running examples in 'palettetown-Ex.R' failed
The error most likely occurred in:

> ### Name: ichooseyou
> ### Title: Get a pokemon palette. Alias for pokepal.
> ### Aliases: ichooseyou
> 
> ### ** Examples
> 
> library(magrittr)
Error in library(magrittr) : there is no package called 'magrittr'
Execution halted
Package required but not available: 'gsl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'tibble', 'ggplot2', 'dplyr', 'tidyr',
  'recipes'
Packages required but not available:
  'dplyr', 'ggplot2', 'dbplyr', 'downloadthis', 'DBI', 'DT',
  'ggplotify', 'ggwordcloud', 'ggExtra', 'gridExtra', 'htmltools',
  'htmlwidgets', 'leaflet', 'plotly', 'rmarkdown', 'RPostgreSQL',
  'scales', 'viridisLite'

Packages suggested but not available for checking:
  'sf', 'rnaturalearth', 'rnaturalearthdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'gsl', 'minqa', 'mvtnorm', 'R6'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'partykit', 'Formula'

Packages suggested but not available for checking: 'mvtnorm', 'psychotools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'raster', 'testthat', 'covr', 'stars',
  'viridis'

VignetteBuilder package required for checking but not installed: 'knitr'
Running examples in 'palr-Ex.R' failed
The error most likely occurred in:

> ### Name: image_pal
> ### Title: Map data values to colours
> ### Aliases: image_pal image_raster image_stars
> 
> ### ** Examples
> 
> set.seed(28)
> vals <- sort(rnorm(100))
> cols <- image_pal(vals, zlim = c(-2.4, 2))
> plot(vals, col = cols); abline(h = 2)
> points(vals, pch  = 19, cex = 0.1) ## zlim excluded some of the range
> if (requireNamespace("raster", quietly = TRUE)) {
+ im <- image_raster(volcano)
+ library(raster)
+ plotRGB(im)
+ }
> if (!requireNamespace("stars", quietly = TRUE)) {
+ library(stars)
+ x <- st_as_stars(volcano)
+ plot(image_stars(x), rgb = 1:3)
+ }
Error in library(stars) : there is no package called 'stars'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dichromat', 'colorspace', 'mapproj', 'maps'

Packages suggested but not available for checking:
  'classInt', 'ggplot2', 'knitr', 'latticeExtra', 'reshape2', 'rgl',
  'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ExtMallows', 'mc2d', 'PerMallows', 'rankdist', 'Rcpp'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ade4', 'xtable', 'FactoClass'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
Packages required but not available:
  'heatmapFlex', 'RColorBrewer', 'R.utils', 'readxl', 'readmoRe',
  'plyr', 'robustHD'

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', 'tuneR', 'seewave', 'dplyr', 'magrittr', 'RcppRoll',
  'PamBinaries', 'RSQLite', 'lubridate', 'rerddap', 'ncdf4', 'httr',
  'purrr', 'xml2', 'hoardr', 'geosphere', 'stringr', 'viridisLite',
  'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lmerTest', 'mvtnorm', 'lme4'

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'magrittr', 'rlang', 'tidyr', 'ggplot2', 'dplyr',
  'purrr', 'tibble', 'lazyeval', 'Formula', 'mvtnorm', 'pec', 'vctrs'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'PamBinaries', 'PAMmisc', 'dplyr', 'tuneR', 'seewave', 'gam',
  'data.table', 'RSQLite', 'stringr', 'purrr', 'signal', 'tidyr',
  'ggplot2', 'manipulate', 'knitr', 'rstudioapi', 'xml2', 'rlang',
  'reticulate', 'lubridate'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'leaps'

Package which this enhances but not available for checking: 'xtable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'coin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mvtnorm', 'smoothmest', 'msm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'rstantools', 'Rcpp', 'plotly', 'dplyr', 'curl', 'tidyr',
  'covid19br', 'BH', 'RcppEigen', 'RcppParallel', 'StanHeaders'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'webshot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'digest', 'Rcpp'

Packages suggested but not available for checking:
  'ggplot2', 'sylly', 'sylly.en', 'logger', 'microbenchmark', 'zoo',
  'descr', 'knitr', 'rmarkdown', 'tables', 'reshape', 'memisc', 'Epi',
  'randomForest', 'tseries', 'gtable', 'rms', 'forecast', 'data.table'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'jsonlite'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/pandocfilters.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'statmod', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Paneldata.formula: no visible global function definition for
  'model.frame'
Paneldata.formula: no visible global function definition for
  'model.matrix'
Paneldata.formula: no visible global function definition for
  'model.response'
summary.Paneldata: no visible global function definition for 'coef'
summary.Paneldata: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Packages required but not available:
  'Rcpp', 'data.table', 'ggplot2', 'CBPS', 'igraph', 'RcppArmadillo',
  'RcppEigen'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'crayon', 'dplyr', 'Formula', 'ggplot2', 'jtools',
  'lmerTest', 'magrittr', 'purrr', 'rlang', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'car', 'clubSandwich', 'geepack', 'generics',
  'plm', 'sandwich', 'skimr', 'tidyr', 'testthat', 'covr', 'knitr',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'knitr', 'progress', 'matrixcalc', 'texreg', 'ggplot2', 'reshape2'

Package suggested but not available for checking: 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'Hmisc', 'caret'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crul', 'jsonlite', 'xml2', 'oai', 'tibble', 'hoardr', 'png'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'vcr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'mitools', 'lme4'
Packages required but not available:
  'attempt', 'dplyr', 'glue', 'httr', 'jsonlite', 'magrittr', 'purrr',
  'RCurl', 'readr', 'rlang', 'stringr'

Packages suggested but not available for checking:
  'celestial', 'FITSio', 'knitr', 'magicaxis', 'magick', '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', 'tibble'

VignetteBuilder package required for checking but not installed: 'knitr'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Packages required but not available:
  'neurobase', 'oro.nifti', 'servr', 'htmltools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyverse', 'binom', 'PropCIs', 'ratesci', 'Hmisc',
  'shiny', 'shinythemes', 'readxl', 'DT'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'xtable', 'gmodels'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

Package which this enhances but not available for checking: 'lme4'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/papeR_with_latex.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'checkmate', 'data.table', 'mlr3misc', 'R6'

Packages suggested but not available for checking:
  'knitr', 'lhs', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'RcppArmadillo'

Packages suggested but not available for checking:
  'dtw', 'ggplot2', 'proxy', 'testthat', 'RcppArmadillo',
  'RcppXPtrUtils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'snowfall', 'raster', 'sp', 'pryr', 'caret', 'geoR', 'gstat',
  'quantregForest', 'randomForest', 'stringr', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'snow', 'xml2', 'jsonlite'

Packages suggested but not available for checking:
  'mailR', 'testthat', 'shiny', 'DT', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BBmisc', 'checkmate'

Packages suggested but not available for checking:
  'BatchJobs', 'batchtools', 'data.table', 'Rmpi', 'snow', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mvtnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'foreach', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'bnlearn', 'pcalg', 'Rgraphviz'
Running examples in 'ParallelPC-Ex.R' failed
The error most likely occurred in:

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)
Error in library(bnlearn) : there is no package called 'bnlearn'
Execution halted
Package required but not available: 'htmlwidgets'

Packages suggested but not available for checking:
  'testthat', 'shiny', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'checkmate', 'data.table', 'dictionar6', 'set6', 'R6'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bayestestR', 'datawizard', 'insight'

Packages suggested but not available for checking:
  'AER', 'afex', 'aod', 'BayesFactor', 'BayesFM', 'bbmle', 'betareg',
  'biglm', 'blme', 'brglm2', 'brms', 'broom', 'cAIC4', 'car', 'cgam',
  'ClassDiscovery', 'clubSandwich', 'cplm', 'dbscan', 'drc', 'DRR',
  'effectsize', 'EGAnet', 'emmeans', 'factoextra', 'FactoMineR',
  'fastICA', 'fixest', 'fpc', 'gam', 'gamlss', 'gee', 'geepack',
  'ggplot2', 'GLMMadaptive', 'glmmTMB', 'GPArotation', 'gt', 'httr',
  'ivprobit', 'ivreg', 'knitr', 'lavaan', 'lavaSearch2', 'lfe',
  'lm.beta', 'lme4', 'lmerTest', 'lmtest', 'logspline', 'lqmm', 'M3C',
  'magrittr', 'mclust', 'MCMCglmm', 'mediation', 'metaBMA', 'metafor',
  'mfx', 'mice', 'multcomp', 'MuMIn', 'NbClust', 'nFactors',
  'openxlsx', 'ordinal', 'panelr', 'pbkrtest', 'PCDimension',
  'performance', 'plm', 'PMCMRplus', 'poorman', 'PROreg', 'projpred',
  'pscl', 'psych', 'pvclust', 'quantreg', 'randomForest', 'rmarkdown',
  'rstanarm', 'sandwich', 'see', 'sjstats', 'spelling', 'survey',
  'testthat', 'TMB', 'tripack', 'truncreg', 'VGAM', 'WRS2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TIMP', 'shiny', 'shinydashboard', 'colorspace', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'backports', 'BBmisc', 'checkmate', 'fastmatch'

Packages suggested but not available for checking:
  'akima', 'covr', 'eaf', 'emoa', 'GGally', 'ggplot2', 'gridExtra',
  'irace', 'lhs', 'plyr', 'reshape2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggpubr', 'lme4', 'survey'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pedtools', 'pedprobr'

Packages suggested but not available for checking: 'spelling', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'assertthat', 'kinship2', 'maxLik'

Packages suggested but not available for checking: 'identity', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'whisker', 'RcppTOML', 'glue', 'readr', 'purrr'

Packages suggested but not available for checking:
  'openxlsx', 'testthat', 'knitr', 'utf8'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'beepr', 'pwr', 'ggplot2', 'knitr', 'lavaan', 'dplyr', 'testthat',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'data.table', 'DiceKriging', 'foreach', 'dbscan', 'lhs', 'crayon',
  'ggplot2', 'ggpubr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'xgboost', 'doParallel', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mboost', 'party', 'iterators', 'plyr', 'caret', 'glmnet',
  'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'easyalluvial', 'tidyr', 'dplyr', 'purrr', 'forcats', 'magrittr',
  'tibble', 'htmlwidgets', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'randomForest', 'knitr', 'rmarkdown', 'spelling',
  'plotly', 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'crosstalk', 'htmlwidgets'

Packages suggested but not available for checking:
  'd3r', 'ggplot2', 'htmltools', 'knitr', 'shiny', 'testthat',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'DNAcopy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ADGofTest', 'lmom', 'foreach', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'lpSolve'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'optimx', 'msm', 'sn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'SuppDists', 'knitr', 'rmarkdown', 'speedglm',
  'microbenchmark', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'matrixStats', 'RNifti', 'plyr', 'ARIbrain', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gridExtra'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'hansard', 'mnis', 'dplyr', 'stringi', 'sf', 'snakecase', 'readr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'covr', 'rgdal', 'devtools',
  'leaflet', 'htmltools', 'cartogram', 'htmlwidgets', 'ggplot2',
  'tibble', 'janitor'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'nloptr', 'slam', 'Rglpk', 'quadprog', 'corpcor', 'truncnorm'

Packages suggested but not available for checking: 'xts', 'Rsymphony'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fitdistrplus', 'flexsurv', 'ggplot2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'purrr', 'arrow', '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: 'igraph', 'netrankr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'covr', 'testthat', 'withr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'RSelenium', 'lubridate', 'purrr'

Packages suggested but not available for checking:
  'rmarkdown', 'knitr', 'testthat', 'covr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'purrr', 'Rcpp', 'cli', 'checkmate', 'readr', 'tidyr', 'dplyr',
  'tibble', 'yaml', 'withr', 'rmarkdown', 'pillar', 'rlang',
  'magrittr', 'tidyselect', 'lifecycle', 'BH'

Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'stringr', 'readr', 'doParallel', 'foreach',
  'bigmemory', 'reticulate'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'pbapply', 'snow'

Packages suggested but not available for checking: 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'generics', 'ggplot2', 'globals', 'glue', 'hardhat',
  'lifecycle', 'magrittr', 'prettyunits', 'purrr', 'rlang', 'tibble',
  'tidyr', 'vctrs', 'withr'

Packages suggested but not available for checking:
  'C50', 'covr', 'dials', 'earth', 'tensorflow', 'ggrepel', 'keras',
  'kernlab', 'kknn', 'knitr', 'LiblineaR', 'modeldata', 'ranger',
  'remotes', 'rmarkdown', 'sparklyr', '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: 'ssym', 'optimx'

Packages suggested but not available for checking: 'SMNCensReg', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'TH.data', 'VGAM'
Errors in running code in vignettes:
when running code in 'partDSAvig.Rnw'

> y.out = as.factor(sample(c("a", "b", "c"), 50, TRUE))

> x1 = rexp(50)

> x2 = runif(50)

> library(partDSA)
Loading required package: survival

> y.out.test = as.factor(sample(c("a", "b", "c"), 100, 
+     TRUE))

> x1.test = rexp(100)

> x2.test = runif(100)

> model2 <- partDSA(x = data.frame(x1, x2), y = y.out, 
+     x.test = data.frame(x1 = x1.test, x2 = x2.test), y.test = y.out.test)

> model4 <- partDSA(x = data.frame(x1, x2), y = y.out, 
+     control = DSA.control(missing = "no", cut.off.growth = 2))

> print(model4)
partDSA object
# partitions   mean CV error   sd CV error   test risk
1              0.661667        0.041611      0.640000   
2              0.575000        0.135458      0.560000   

Outcome:
[1] c
Levels: a b c
[1] a c
Levels: a b c

Best 2 partitions
  Partition 1 [of 2]:
    (x1 <= 2.036241)
  Partition 2 [of 2]:
    (2.036241 < x1)

Variable importance matrix:
   COG=1 COG=2
x1     0     2
x2     0     0

> data("GBSG2", package = "TH.data")

  When sourcing 'partDSAvig.R':
Error: there is no package called 'TH.data'
Execution halted
when running code in 'survival.Rnw'

> options(width = 70)

> library(survival)

> T = rexp(25)

> delta = sample(0:1, 25, TRUE)

> y = Surv(T, delta)

> y
 [1] 0.23628326+ 0.30802433  0.38502695+ 0.75921108  0.56170959 
 [6] 1.59112138+ 0.58033950+ 0.38659664+ 0.46746803  1.43268371+
[11] 0.32742997+ 0.53096948+ 2.26567191+ 0.59979091  0.05433469+
[16] 0.01811794  1.04198192+ 0.14272721+ 1.06647663+ 0.01154767+
[21] 1.57118966  0.70511549+ 0.75415087+ 0.28419149+ 0.69834816 

> library(VGAM)

  When sourcing 'survival.R':
Error: there is no package called 'VGAM'
Execution halted

  'partDSAvig.Rnw'... failed
  'survival.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'partDSAvig.Rnw' using Sweave
Loading required package: survival

Error: processing vignette 'partDSAvig.Rnw' failed with diagnostics:
 chunk 7 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'TH.data'

--- failed re-building 'partDSAvig.Rnw'

--- re-building 'survival.Rnw' using Sweave

Error: processing vignette 'survival.Rnw' failed with diagnostics:
 chunk 3 
Error in library(VGAM) : there is no package called 'VGAM'

--- failed re-building 'survival.Rnw'

SUMMARY: processing the following files failed:
  'partDSAvig.Rnw' 'survival.Rnw'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'nnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for 'multinom'
fitOR: no visible global function definition for 'formula'
fitOR: no visible global function definition for 'coef'
fitOR: no visible global function definition for 'optim'
reportOR: no visible global function definition for 'qnorm'
reportOR: no visible global function definition for 'pchisq'
reportOR: no visible global function definition for 'coef'
simData: no visible global function definition for 'rnorm'
simData: no visible global function definition for 'runif'
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available:
  'tidygraph', 'rlang', 'igraph', 'magrittr', 'Rcpp', 'digest', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'ggraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R6', 'rgl'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rdpack', 'lpSolve'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'crayon', 'dplyr', 'forcats', 'ggplot2', 'infotheo', 'magrittr',
  'pillar', 'purrr', 'Rcpp', 'rlang', 'stringr', 'tibble', 'tidyr',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'spelling', 'testthat', 'ggcorrplot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gmp', 'polynom', 'sets', 'mathjaxr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'regtools', 'data.table', 'pdist'

Packages suggested but not available for checking: 'e1071', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'pbapply', 'dplyr', 'purrr', 'rlang', 'tibble', 'magrittr',
  'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'future', 'furrr', 'knitr', 'rmarkdown', 'patchwork',
  'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'libcoin', 'mvtnorm', 'Formula', 'inum'

Packages suggested but not available for checking:
  'XML', 'pmml', 'rJava', 'sandwich', 'strucchange', 'vcd', 'AER',
  'mlbench', 'TH.data', 'coin', 'RWeka', 'psychotools', 'psychotree',
  'party', 'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'mvtnorm', 'modeltools', 'strucchange', 'coin', 'zoo', 'sandwich'

Packages suggested but not available for checking:
  'TH.data', 'mlbench', 'colorspace', 'vcd', 'ipred', 'varImp',
  'randomForest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vioplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'withr'

Packages suggested but not available for checking:
  'testthat', 'randgeo', 'knitr', 'rmarkdown', 'callr', 'pkgbuild',
  'pkgload'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pracma', 'scales'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'betareg', 'rootSolve'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'MKmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'VGAM', 'copBasic', 'pcaPP', 'foreach', 'GGally',
  'gridExtra', 'progress', 'plotly', 'copula', 'Rcpp'

Packages suggested but not available for checking:
  'doParallel', 'tidyverse', 'goftest', 'faraway', 'ordinal', 'rms',
  'testthat', 'PResiduals', 'knitr', 'rmarkdown', 'truncdist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'dplyr', 'DT', 'gapminder', 'ggplot2', 'jsonlite', 'knitr',
  'mockr', 'rmarkdown', 'testthat', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'magrittr', 'dplyr', 'tidyr', 'rlang'

Packages suggested but not available for checking:
  'knitr', 'ggplot2', 'plyr', 'testthat', 'covr', '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: 'svUnit', 'covr'
Running 'test-with-svUnit.R'
Running the tests in 'tests/test-with-svUnit.R' failed.
Complete output:
  > ## Note that the message in case of error is not explicit enough
  > ## Moreover, nothing is printed in case of success, while we would like a succinct report
  > library(svUnit)
  Error in library(svUnit) : there is no package called 'svUnit'
  Execution halted
Packages required but not available: 'caper', 'ape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'e1071'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'knitr'
Package unavailable to check Rd xrefs: 'knitr'
Error(s) in re-building vignettes:
--- re-building 'Japanese.Rnw' using JSweave
Writing to file Japanese.tex
Processing code chunks with options ...

You can now run (pdf)latex on 'Japanese.tex'

Sorry, but C:\PROGRA~1\MiKTeX\miktex\bin\x64\uplatex.exe did not succeed.

The log file hopefully contains the information to get MiKTeX going again:

  C:\Users\ContainerUser\AppData\Local\MiKTeX\miktex\log\uplatex.log
Warning in system(cmd, intern = TRUE) :
  running command '"uplatex" -synctex=1 -interaction=nonstopmode "Japanese.tex"' had status 1
Error: processing vignette 'Japanese.Rnw' failed with diagnostics:
argument to 'which' is not logical
--- failed re-building 'Japanese.Rnw'

--- re-building 'patchDVI.Rnw' using Sweave
--- finished re-building 'patchDVI.Rnw'

SUMMARY: processing the following file failed:
  'Japanese.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'stringr'

Package which this enhances but not available for checking: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'gtable'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'gridGraphics', 'gridExtra', 'ragg',
  'testthat', 'vdiffr', 'covr', 'png'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'lubridate', 'magrittr', 'dplyr', 'rlang', 'xml2', 'progress'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'readr', '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: 'httr', 'jsonlite'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rlang', 'stringi', 'logger'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'config', 'yaml', 'fs', 'magrittr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'shape'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/intro-pathdiagram.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'pathfindR'
Note: found 1 marked UTF-8 string
Packages required but not available:
  'pathfindR.data', 'DBI', 'AnnotationDbi', 'doParallel', 'foreach',
  'rmarkdown', 'org.Hs.eg.db', 'ggplot2', 'ggraph', 'ggupset', 'fpc',
  'igraph', 'R.utils', 'magick', 'msigdbr', 'KEGGREST', 'KEGGgraph',
  'knitr'

Packages suggested but not available for checking: 'testthat', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R6', 'magrittr', 'glue', 'logging', 'rlang', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'jsonlite', 'timeSeries', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lavaan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mice', 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'BART', 'gbm', 'ggplot2', 'metR', 'pryr', 'twang', 'tidyr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'R.matlab', 'data.table', 'magrittr', 'dplyr', 'stringr', 'tibble',
  'tidyr', 'fANCOVA', 'purrr', 'ggplot2', 'tidyselect', 'cowplot'

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:
  'BiocGenerics', 'GenomicFeatures', 'purrr', 'glmnet', 'randomForest',
  'survminer', 'caret', 'data.table', 'RColorBrewer', 'pROC',
  'maftools', 'clusterProfiler'

Packages suggested but not available for checking:
  'stringi', 'knitr', 'rmarkdown', 'testthat', 'BiocManager', 'xfun',
  'e1071', 'qpdf', 'tinytex', 'spelling'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown', 'qpdf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clinUtils', 'ggplot2', 'plyr', 'cowplot', 'reshape2', 'knitr',
  'stringr', 'gridExtra', 'scales'

Packages suggested but not available for checking:
  'pander', 'shiny', 'testthat', 'rmarkdown', 'gtable', 'pdftools',
  '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:
  'reshape2', 'ggplot2', 'gridExtra', 'plyr', 'RColorBrewer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rlang', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'data.table'

Package suggested but not available for checking: 'plyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'raster', 'sp', 'rgdal', 'abind', 'Morpho', 'dplyr', 'imager',
  'magrittr', 'purrr', 'vegan', 'RNiftyReg', 'geomorph', 'ClusterR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'R6', 'ggplot2', 'jpeg', 'png', 'RcppParallel', 'dplyr',
  'gtable', 'gridExtra'

Packages suggested but not available for checking:
  'knitr', 'Cairo', 'RCurl', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'gplots', 'igraph', 'jetset', 'lars', 'limma', 'magic',
  'Mfuzz', 'movMF', 'msgps', 'nnls', 'plotrix', 'SelectBoost', 'tnet',
  'VGAM', 'WGCNA'

Packages suggested but not available for checking:
  'animation', 'Biobase', 'c060', 'elasticnet', 'glmnet', 'pixmap',
  'biomaRt', 'CascadeData', 'repmis', 'knitr', 'R.rsp', 'spls',
  'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'equivalence', 'ggplot2', 'lazyeval', 'lubridate',
  'magrittr', 'matchingMarkets', 'reshape2', 'rlang', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'deSolve', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'future.apply', 'geometry', 'lightr', 'magick', 'farver', 'plot3D',
  'progressr', 'sp', 'viridisLite'

Packages suggested but not available for checking:
  'alphashape3d', 'digest', 'imager', 'knitr', 'mapproj', 'rgl',
  'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'SparseM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'base64enc', 'digest', 'httr', 'jsonlite', 'xml2'

Packages suggested but not available for checking:
  'covr', 'rstudioapi', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'paws.analytics', 'paws.application.integration', 'paws.compute',
  'paws.cost.management', 'paws.customer.engagement', 'paws.database',
  'paws.developer.tools', 'paws.end.user.computing',
  'paws.machine.learning', 'paws.management', 'paws.networking',
  'paws.security.identity', 'paws.storage'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'paws.common'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'shiny'
Package required but not available: 'rootSolve'

Package suggested but not available for checking: 'kinship2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ibd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rlecuyer', 'float'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'deSolve', 'ade4', 'ape', 'DDD', 'phytools'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rlecuyer', 'pbdMPI'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

Packages suggested but not available for checking: 'ggplot2', 'ca'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cmprsk'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'formatR', 'xml2', 'jsonlite', 'zip', 'textclean', 'stringr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'RCurl', 'ggplot2', 'ggraph',
  'igraph', 'imager', 'tidyr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lme4', 'broom', 'dplyr', 'magrittr', 'numDeriv', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'ggplot2', 'gridExtra'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'metaRNASeq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'PerformanceAnalytics', 'foreach', 'latticeExtra', 'testthat',
  'doParallel', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'
'library' or 'require' call to 'foreach' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dotplot.pbo: no visible global function definition for 'reorder'
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
pbo: no visible global function definition for 'lm'
xyplot.pbo: no visible global function definition for 'ecdf'
xyplot.pbo: no visible global function definition for 'doubleYScale'
xyplot.pbo: no visible global function definition for 'reorder'
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
Running 'test_pbo_function.R'
Running the tests in 'tests/test_pbo_function.R' failed.
Complete output:
  > # unit tests for pbo 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require(pbo)
  Loading required package: pbo
  Loading required package: lattice
  > 
  > context("Function usage")
  Error in context("Function usage") : could not find function "context"
  Execution halted
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: 'PBSmodelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'PBSmodelling'
Packages suggested but not available for checking: 'maptools', 'deldir'
Running examples in 'PBSmapping-Ex.R' failed
The error most likely occurred in:

> ### Name: calcVoronoi
> ### Title: Calculate the Voronoi (Dirichlet) Tesselation for a Set of
> ###   Points
> ### Aliases: calcVoronoi
> ### Keywords: manip
> 
> ### ** Examples
> 
> local(envir=.PBSmapEnv,expr={
+   oldpar = par(no.readonly=TRUE)
+   #--- create some EventData
+   events <- as.EventData(data.frame(
+     EID=1:200, X=rnorm(200), Y=rnorm(200)), projection=1)
+   #--- calculate the Voronoi tesselation
+   polys <- calcVoronoi(events)
+   #--- create PolyData to color it based on area
+   polyData <- calcArea(polys)
+   names(polyData)[is.element(names(polyData), "area")] <- "Z"
+   colSeq <- seq(0.4, 0.95, length=4)
+   polyData <- makeProps(polyData,
+     breaks=quantile(polyData$Z,c(0,.25,.5,.75,1)),
+     propName="col", propVals=rgb(colSeq,colSeq,colSeq))
+   #--- plot the tesselation
+   plotMap(polys, polyProps=polyData)
+   #--- plot the points
+   addPoints(events, pch=19)
+   par(oldpar)
+ })
Loading required package: deldir
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'deldir'
Error in .checkRDeps("calcVoronoi", c("deldir")) : 
The function 'calcVoronoi' requires the package(s) 'deldir'.
Please install the package(s) and try again.
Calls: local ... eval -> eval -> eval -> eval -> calcVoronoi -> .checkRDeps
Execution halted
Package required but not available: 'XML'

Packages suggested but not available for checking: 'PBSmapping', 'deSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'pbivnorm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgl', 'ellipse'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'FactoMineR', 'RColorBrewer'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigutilsr', 'data.table', 'ggplot2', 'magrittr', 'mmapcharr',
  'Rcpp', 'RSpectra', 'rmio'

Packages suggested but not available for checking:
  'plotly', 'shiny', 'spelling', 'testthat', 'vcfR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'reshape2', 'pander', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'abind', 'graph', 'RBGL', 'igraph', 'ggm', 'corpcor', 'robustbase',
  'vcd', 'Rcpp', 'bdsmatrix', 'sfsmisc', 'fastICA', 'clue',
  'RcppArmadillo', 'BH'

Packages suggested but not available for checking:
  'Rgraphviz', 'mvtnorm', 'huge', 'ggplot2', 'dagitty'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'exact2x2', 'MCMCpack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rdpack'

Packages suggested but not available for checking:
  'covr', 'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'optmatch', 'testthat', 'knitr', 'rmarkdown', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
Package required but not available: 'mvtnorm'

Package suggested but not available for checking: 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'httr', 'jsonlite', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'knitr', 'rmarkdown', 'testthat', 'readr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ClassDiscovery', 'oompaBase', 'kernlab', 'changepoint', 'cpm'

Package suggested but not available for checking: 'nFactors'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'freqdom', 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'combinat', 'interp', 'plot3D', 'plotrix', 'Rdpack'

Packages suggested but not available for checking:
  'scatterplot3d', 'spatstat.random'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'RMTstat', 'corpcor'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/pcev.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'reshape2', 'mvtnorm', 'igraph',
  'loo', 'lifecycle', 'RcppEigen', 'RcppParallel', 'StanHeaders', 'BH'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'shiny', 'ggplot2', 'covr',
  'qgraph'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pcalg', 'graph', 'Hmisc', 'lme4', 'sommer', 'ggm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'safe', 'RMTstat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bigstatsr', 'bnlearn', 'Rfast', 'Rfast2', 'robustbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'RUnit'
Running 'bootstrap.R'
  Running 'test_functions.R'
Running the tests in 'tests/test_functions.R' failed.
Complete output:
  > library(PCICt)
  > library(RUnit)
  Error in library(RUnit) : there is no package called 'RUnit'
  Execution halted
Packages required but not available: 'Rcpp', 'combinat'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'svd'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'grpreg'

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:
  'ape', 'distory', 'geiger', 'mvSLOUCH', 'phangorn', 'TreeSim',
  'yuima'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'PCMBase', 'data.table', 'abind', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ape', 'expm', 'mvtnorm', 'data.table', 'ggplot2', 'xtable'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'abind', 'ggtree', 'cowplot',
  'covr', 'mvSLOUCH', 'BiocManager'

VignetteBuilder packages required for checking but not installed:
  'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ltm', 'statmod', 'cubature', 'mvtnorm', 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rjags', 'coda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'fda', 'pracma', 'deSolve'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'Hmisc', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GPArotation', 'ThreeWay'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'doParallel', 'foreach', 'ggplot2', 'prodlim',
  'riskRegression', 'PermAlgo', 'pec', 'RcppArmadillo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'SYNCSA', 'ape', 'picante', 'phylobase', 'vegan', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bcp', 'changepoint', 'chipPCR', 'ecp', 'fda.usc', 'MBmca',
  'pbapply', 'pracma', 'qpcR', 'robustbase', 'segmented', 'shiny',
  'zoo'

Packages suggested but not available for checking:
  'DT', 'future', 'knitr', 'listenv', 'RDML', 'readxl', 'rmarkdown',
  'shinycssloaders', 'spelling', 'testthat', 'xtable'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'covr', 'cowplot'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'testthat'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'statmod', 'multtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'gtools', 'Rdpack'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'igraph'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'stplanr', 'readr', 'sf'

Packages suggested but not available for checking:
  'covr', 'curl', 'dplyr', 'ggplot2', 'knitr', 'leaflet', 'pbapply',
  'remotes', 'rmarkdown', 'testthat', 'tmap', 'bookdown', '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:
  'sarima', 'BB', 'PolynomF', 'gbutils', 'zoo', 'xts', 'lagged',
  'mcompanion', 'Rdpack', 'lubridate'

Packages suggested but not available for checking:
  'testthat', 'fUnitRoots', 'partsm', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'httr', 'rvest', 'jsonlite', 'data.table', 'RcppArmadillo'

Package suggested but not available for checking: 'imager'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'plotrix'
Package required but not available: 'tcltk2'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plm'

Packages suggested but not available for checking:
  'car', 'dplyr', 'ggplot2', 'lmtest', 'msm', 'pglm', 'splm', 'texreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geometry'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'httr', 'zoo', 'xts', 'XML', 'lubridate', 'jsonlite', 'reshape2',
  'curl', 'xml2', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'checkmate', 'jsonlite'

Packages suggested but not available for checking: 'PythonInR', 'RSQLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pdftools', 'tibble', 'tokenizers', 'stringi'

Packages suggested but not available for checking:
  'shiny', 'testthat', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'httr'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'qpdf'

Packages suggested but not available for checking:
  'png', 'webp', 'tesseract', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'magrittr', 'purrr', 'randomForest', 'readxl', 'stringr',
  'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'covr', 'knitr', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pdist: no visible global function definition for 'dist'
pdist: no visible global function definition for 'new'
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'diagonals', 'ncvreg', 'quantreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mco'

Package suggested but not available for checking: 'RUnit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'jpeg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'glmnet', 'ggplot2', 'network'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plyr', 'dendextend', 'tseries'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'gridExtra', 'magrittr', 'plyr', 'viridis'

Packages suggested but not available for checking:
  'adabag', 'AmesHousing', 'C50', 'caret', 'Cubist', 'doParallel',
  'dplyr', 'e1071', 'earth', 'gbm', 'ipred', 'keras', 'kernlab', 'mda',
  'party', 'partykit', 'progress', 'randomForest', 'ranger',
  'testthat', 'xgboost', 'knitr', 'rmarkdown', 'vip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'covr', 'knitr', 'pillar', 'rmarkdown', 'spelling', 'testthat',
  'vdiffr'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'orthopolynom', 'moments'

Packages suggested but not available for checking:
  'ggplot2', 'reshape2', 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/PDQutils.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plm', 'car', 'coefplot', 'lmtest', 'sandwich', 'papeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rly'

Packages suggested but not available for checking:
  'testthat', 'covr', 'lintr', 'knitr', 'curl', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
band.chol.cv: no visible global function definition for 'cov'
pdsoft.cv: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Package required but not available: 'shiny'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'multitaper', 'Rcpp', 'ddalpha', 'Rdpack', 'RcppArmadillo'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'testthat', 'ggplot2', 'reshape2', 'viridis',
  'ggthemes'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'monobin', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'magrittr', 'rlang', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'leaflet', 'leaflet.extras', 'gganimate',
  'infer', 'moderndive', 'readr', 'gifski', 'ggplot2', 'forcats'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'optimx', 'qlcMatrix', 'Rdpack'

Packages suggested but not available for checking:
  'pder', 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'magrittr', 'dplyr', 'geosphere', 'tidyr', 'stringr', 'rlang',
  'stevemisc', 'lifecycle'

Packages suggested but not available for checking:
  'countrycode', 'tibble', 'testthat', 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mnormt', 'metap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running examples in 'PeakError-Ex.R' failed
The error most likely occurred in:

> ### Name: PeakError
> ### Title: PeakError
> ### Aliases: PeakError
> 
> ### ** Examples
> 
> x <- seq(5, 85, by=5)
> peaks <- rbind(Peaks("chr2", x, x+3),
+                Peaks("chr3", c(25, 38, 57), c(33, 54, 75)),
+                Peaks("chr4", c(5, 32, 38, 65), c(15, 35, 55, 85)),
+                Peaks("chr5", c(12, 26, 56, 75), c(16, 54, 59, 85)))
> regions <- NULL
> for(chr in 1:5){
+   regions <- rbind(regions, {
+     data.frame(chrom=paste0("chr", chr),
+                chromStart=c(10, 30, 50, 70),
+                chromEnd=c(20, 40, 60, 80),
+                annotation=c("noPeaks", "peakStart", "peakEnd", "peaks"))
+   })
+ }
> err <- PeakError(peaks, regions)
> ann.colors <-
+   c(noPeaks="#f6f4bf",
+     peakStart="#ffafaf",
+     peakEnd="#ff4c4c",
+     peaks="#a445ee")
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Running 'testthat.R'
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: 'matrixStats'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'
'LazyData' is specified without a 'data' directory
Package required but not available: 'data.table'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'future.apply', 'future', 'knitr', 'markdown'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Examples.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'penaltyLearning'
Running examples in 'PeakSegDP-Ex.R' failed
The error most likely occurred in:

> ### Name: chr11ChIPseq
> ### Title: ChIP-seq aligned read coverage for 4 samples on a subset of
> ###   chr11
> ### Aliases: chr11ChIPseq
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(chr11ChIPseq)
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'PeakError', 'penaltyLearning'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'microbenchmark'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'penaltyLearning'

Packages suggested but not available for checking:
  'PeakSegDP', 'ggplot2', 'testthat', 'data.table'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'gsl'
Package unavailable to check Rd xrefs: 'gsl'
Packages required but not available: 'Rcpp', 'matrixStats', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'prodlim', 'foreach', 'rms', 'riskRegression', 'lava', 'timereg'

Packages suggested but not available for checking:
  'party', 'cmprsk', 'Hmisc'

Packages which this enhances but not available for checking:
  'crrstep', 'randomForestSRC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'car', 'data.table', 'digest', 'dplyr', 'ggplot2', 'htmltools',
  'knitr', 'lubridate', 'qwraps2', 'scales', '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:
  'pedtools', 'pedprobr', 'forrel', 'glue'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'CompQuadForm', 'survey', 'kinship2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'HaploSim', 'reshape'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'BH', 'testthat'

Packages suggested but not available for checking:
  'testthat', 'mvtnorm', 'xml2', 'knitr', 'rmarkdown', 'R.rsp',
  'abind', 'kinship2', 'igraph'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: '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: 'pedtools', 'pedmut'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'data.table', 'TTR', 'zoo', 'PerformanceAnalytics', 'curl', 'xml2',
  'httr', 'rvest', 'webdriver', 'jsonlite', 'stringi', 'readxl',
  'readr', 'ggplot2', 'scales', 'gridExtra', 'plotly'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'forrel', 'pedprobr', 'pedtools', 'ribd', 'verbalisr', 'pedmut',
  'dvir', 'ibdsim2', 'paramlink2', 'pedbuildr', 'segregatr'

Packages suggested but not available 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: 'kinship2'

Packages suggested but not available for checking:
  'igraph', 'kableExtra', 'knitr', 'pedmut', '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', 'curl', 'httr2', 'stringr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sandwich', 'lmtest'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ape'

Packages suggested but not available for checking:
  'rgl', 'snpStats', 'adegenet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bvls', 'RSEIS', 'pracma', 'geigen', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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: 'DT', 'htmlwidgets', 'shiny'

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:
  'rstan', 'Rcpp', 'RcppParallel', 'rstantools', 'sn', 'BH',
  'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
PEMM_fun : find.lambda: no visible global function definition for
  'optimize'
PEMM_fun: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
Packages required but not available:
  'loa', 'RColorBrewer', 'latticeExtra', 'baseline', 'ggplot2',
  'rlang', 'dplyr', 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'irlba', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'penalized', 'clogitL1', 'tidyverse'

Packages suggested but not available for checking: 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'flsa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: 'globaltest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'e1071', 'mlegp', 'corpcor', 'statmod', 'tgp', 'lhs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'data.table', 'ggplot2'

Packages suggested but not available for checking:
  'neuroblastoma', 'jointseg', 'testthat', 'future', 'future.apply',
  'directlabels'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'foreach', 'doParallel', 'glmnet', 'survcomp', 'survivalROC',
  'dplyr', 'magic', 'lcmm'

Packages suggested but not available for checking:
  'ptmixed', 'survminer', 'knitr', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fda', 'latticeExtra', 'pacotest', 'quadprog', 'doParallel',
  'foreach', 'TSP', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'TSP', 'fda', 'foreach', 'quadprog', 'latticeExtra', 'doParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GJRM', 'trust'

Packages suggested but not available for checking:
  'cartography', 'knitr', 'plotly', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'numDeriv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'Rdpack', 'RcppArmadillo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'glmnet', 'fixest', 'collapse', 'rlang', 'magrittr',
  'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'directlabels', 'ggplot2',
  'reshape2'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'Rcpp', 'lifecycle', 'rlang', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'jsonlite'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'penalized'

Packages suggested but not available for checking:
  'survivalROC', 'rmarkdown', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'snowfall'

Packages suggested but not available for checking: 'locfit', 'penalized'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'yaml', 'stringr', 'pryr', 'data.table'

Packages suggested but not available for checking:
  'knitr', 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'elasticnet'

Packages suggested but not available for checking: 'testthat', 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/Paper_Analysis.Rnw'
   'inst/doc/PepSAVIms_Introduction.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'discreteRV', 'plyr', 'dplyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Rcpp'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'corpcor', 'gnm', 'matlab', 'signal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'multcomp'

Packages suggested but not available for checking:
  'magrittr', 'spelling', 'dplyr', 'knitr', 'rmarkdown', 'testthat',
  'ggplot2', 'carData', 'tidyr', 'covr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppEigen'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'assertive.types', 'assertthat', 'R6'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'knitr', 'rmarkdown', 'devtools', 'reshape2'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ape', 'phytools', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'HHG', 'dendextend', 'vcfR', 'R.rsp'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ltm', 'mirt', 'fda', 'Hmisc', 'irtoys'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'limma', 'graph', 'RBGL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xts', 'quadprog', 'zoo'

Packages suggested but not available for checking:
  'dygraphs', 'Hmisc', 'quantmod', 'gamlss', 'gamlss.dist',
  'robustbase', 'quantreg', 'tinytest', 'ggplot2', 'RColorBrewer',
  'googleVis', 'plotly', 'gridExtra', 'ggpubr', 'RPESE', 'R.rsp',
  'RobStatTM'

VignetteBuilder package required for checking but not installed: 'R.rsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'parallelMap', 'tidyr', 'dplyr'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'devtools', 'e1071', 'DMwR', 'randomForest',
  'quantmod', 'mlbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bayestestR', 'insight', 'datawizard'

Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFactor', 'betareg', 'bigutilsr', 'brms', 'car',
  'CompQuadForm', 'correlation', 'cplm', 'dbscan', 'dplyr', 'fixest',
  'forecast', 'gamm4', 'ggplot2', 'glmmTMB', 'ICS', 'ICSOutlier',
  'ISLR', 'lavaan', 'lme4', 'lmtest', 'loo', 'magrittr', 'mclust',
  'metafor', 'mlogit', 'multimode', 'nonnest2', 'ordinal',
  'parameters', 'patchwork', 'pscl', 'psych', 'randomForest',
  'rmarkdown', 'rstanarm', 'rstantools', 'sandwich', 'see', 'spelling',
  'survey', 'testthat', 'tweedie', 'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'seriation'

Packages suggested but not available for checking:
  'knitr', 'gclus', 'dendextend', 'dendextendRcpp', 'rmarkdown'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'rms'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinyBS', 'lubridate', 'DT', 'writexl',
  'ggplot2', 'fresh', 'yaml'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'shinydashboardPlus', 'testthat',
  'canvasXpress', 'openxlsx', 'colourpicker'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
permalgorithm: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: 'Rcpp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'xtable', 'scales', 'deldir'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'coin'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ipred', 'party', 'randomForest'

Packages suggested but not available for checking:
  'knitr', 'rmarkdown', 'scales', 'testthat'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'R2HTML', 'xtable'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

Files named as vignettes but with no recognized vignette engine:
   'inst/doc/permPATHmanual.Rnw'
(Is a VignetteBuilder field missing?)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'coin'
Running 'perm.coin.check.R'
Running the tests in 'tests/perm.coin.check.R' failed.
Complete output:
  > ## check perm against coin (ver 1.0-8 or greater)
  > library(perm)
  > library(coin)
  Error in library(coin) : there is no package called 'coin'
  Execution halted
Packages required but not available:
  'ggplot2', 'rlang', 'dabestr', 'gridExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'permute', 'Rcpp'

Packages suggested but not available for checking:
  'R.rsp', 'testthat', 'covr', '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: 'magic', 'numbers', 'partitions'

Package suggested but not available for checking: 'knitr'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'vegan', 'testthat', 'knitr', 'rmarkdown', 'bookdown', 'sessioninfo'

VignetteBuilder package required for checking but not installed: 'knitr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## Test `permute` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: 'plyr'

Packages suggested but not available for checking:
  'buildmer', 'car', 'doParallel', 'dplyr', 'ggplot2', 'lmPerm',
  'lme4', 'permuco', 'knitr', 'rmarkdown', 'viridis'

VignetteBuilder package required for checking but not installed: 'knitr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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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'
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Malformed Description field: should contain one or more complete sentences.
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manual.
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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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  'rlang', 'rlist', 'stringr', 'tibble'

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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'
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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'
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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'
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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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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.
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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.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'VIM', 'bbmle', 'gridExtra', 'mice', 'nortest', 'outliers', 'plotly',
  'psych', 'purrr', 'rcompanion', 'readr', 'readxl', 'rJava', 'rlang',
  'rmarkdown', 'robust', 'shiny', 'shinydashboard', 'shinyjs',
  'shinyWidgets', 'stringr', 'tibble', 'tidyr', 'tidyselect', 'writexl'

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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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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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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'
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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'
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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.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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  'zoo', 'gridExtra', 'ggplot2', 'optimx', 'ucminf', 'numDeriv',
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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See section 'The DESCRIPTION file' in the 'Writing R Extensions'
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  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lme4', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
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  'data.table', 'Rcpp', 'cowplot', 'ggplot2', 'reshape2', 'dplyr'

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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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  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
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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'
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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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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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Running examples in 'phylin-Ex.R' failed
The error most likely occurred in:

> ### Name: extract.val
> ### Title: Extact pairwise values from a matrix in a specified order.
> ### Aliases: extract.val
> ### Keywords: variogram kriging
> 
> ### ** Examples
> 
> 
> data(vipers)
> data(d.gen)
> 
> # calculate midpoints
> mp <- midpoints(vipers[,1:2])
Error in midpoints(vipers[, 1:2]) : 
  Package 'geometry' is needed for Delaunay triangulation.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'phylin_tutorial.Snw' using Sweave

Error: processing vignette 'phylin_tutorial.Snw' failed with diagnostics:
 chunk 31 (label = midpoints) 
Error in midpoints(vipers[, 1:2]) : 
  Package 'geometry' is needed for Delaunay triangulation.

--- failed re-building 'phylin_tutorial.Snw'

--- re-building 'resistance_tutorial.Snw' using Sweave

Error: processing vignette 'resistance_tutorial.Snw' failed with diagnostics:
 chunk 7 (label = conductanceraster) 
Error in library(gdistance) : there is no package called 'gdistance'

--- failed re-building 'resistance_tutorial.Snw'

SUMMARY: processing the following files failed:
  'phylin_tutorial.Snw' 'resistance_tutorial.Snw'

Error: Vignette re-building failed.
Execution halted