Packages required but not available: 'weights', 'plyr', 'survey', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'DT', 'shiny', 'shinycssloaders', 'shinydashboard', 'shinyFeedback',
  'shinyjs', 'shinyWidgets'

Package suggested but not available for checking: ‘plumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'quanteda', 'spacyr', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking:
  'DTRlearn2', 'glmnet', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'brms', 'repmis'

Packages suggested but not available for checking:
  'rstan', 'pollimetrydata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'DT', 'RcppCWB'

Packages suggested but not available for checking:
  'shiny', 'shinythemes', 'shinyjs', 'miniUI', 'tidytext', 'protolite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'sf', 'leaflet', 'geojsonsf', 'shinydashboard', 'DT',
  'leaflet.extras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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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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  'reshape2', 'polyRAD', 'updog', 'mappoly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) inputData.Rd:94: Lost braces
    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
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    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) preprocessData.Rd:81: Lost braces
    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) preprocessData.Rd:82: Lost braces
    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) stat_quantile_prob.Rd:14: Lost braces; missing escapes or markup?
    14 | Number {25, 50, 75}
       |        ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

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', 'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking: 'mappoly', 'polymapR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'ade4', 'adegenet', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) calculateDIC.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateDIC.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polySegratioMM-package.Rd:70-72: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'Rcpp'

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.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'pROC', 'ipred'

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

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

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ape', 'phangorn', 'phylolm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'poolHelper', 'scrm'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘scrm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘later’

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'brms', 'lme4', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘magick’
checkRd: (-1) plot.tfam.Rd:17: Lost braces
    17 | objects created using code{tfam_inertia}.}
       |                           ^
checkRd: (-1) popdemo-package.Rd:32: Lost braces
    32 |        code{\link{inertia}} measures asymptotic population density relative to stable
       |            ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |     ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |              ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘popdemo.Rmd’ using rmarkdown

Quitting from lines 94-99 [unnamed-chunk-4] (popdemo.Rmd)
Error: processing vignette 'popdemo.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building ‘popdemo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GA', 'Rcpp', 'shiny', 'devtools', 'mrgsolve'
Package required but not available: ‘Epi’

Package suggested but not available for checking: ‘relsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'scatterpie', 'spdep', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'gap', 'plyr', 'dismo', 'reshape2', 'ade4', 'pegas',
  'gdistance', 'mmod', 'GGally', 'raster'

Package suggested but not available for checking: ‘sf’

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

Package suggested but not available for checking: ‘bnpsd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'ape', 'ade4', 'pegas', 'polysat', 'shiny'

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: ‘reshape’
Note: skipping ‘burkina-faso-females.Rnw’ due to unavailable dependencies:
  'reshape'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'demography', 'forecast', 'ggpubr', 'DescTools', 'rcompanion',
  'corrr', 'rainbow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'devtools', 'plyr', 'shiny', 'shinycssloaders'

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

Package suggested but not available for checking: ‘areal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rags2ridges’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'osqp', 'CVXR', 'GSE'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'CVXR', 'DT', 'readtext'
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rugarch', 'rvinecopulib', 'kde1d', 'RcppEigen', 'wdm'

Package suggested but not available for checking: ‘ggtext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rxode2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘faux’
Packages required but not available: 'katex', 'prismjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pagedown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'RcppEigen', 'rstan'
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > testthat::test_check("PosteriorBootstrap")
  Loading required package: PosteriorBootstrap
  Welcome to PosteriorBootstrap, a parallel approach for adaptive non-parametric learning
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 31 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test_german_data.R:39:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_anpl.R:5:1'): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library("rstan")`: there is no package called 'rstan'
  Backtrace:
      ▆
   1. └─base::library("rstan") at test_anpl.R:5:1
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 31 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PosteriorBootstrap.Rmd’ using rmarkdown_notangle

Quitting from lines 54-61 [unnamed-chunk-1] (PosteriorBootstrap.Rmd)
Error: processing vignette 'PosteriorBootstrap.Rmd' failed with diagnostics:
there is no package called 'rstan'
--- failed re-building ‘PosteriorBootstrap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'caret', 'ggdist'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'refund', 'cosinor', 'cosinor2', 'accelerometry', 'ActCR', 'ActFrag',
  'GGIR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘crul’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mcmcse’

Package suggested but not available for checking: ‘rstan’

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

Packages suggested but not available for checking:
  'lwgeom', 'eurostat', 'giscoR', 'mapsf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘netmeta’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'gap', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ape', 'lamW', 'adaptMCMC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'openxlsx', 'reshape2', 'HLMdiag', 'saeRobust', 'spdep',
  'bestNormalize', 'survey', 'sf'

Package suggested but not available for checking: ‘simFrame’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'plyr', 'reshape', 'plotly', 'ggpubr', 'shiny', 'DT', 'shinyWidgets',
  'FactoMineR', 'factoextra', 'rxylib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PowerTOST', 'cubature'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'phytools', 'treebalance', 'diversitree'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'lme4', 'reshape2', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Seurat', 'plotly', 'rayshader'

Packages suggested but not available for checking: 'fields', 'rayrender'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) coalesce_xy.Rd:22: Lost braces; missing escapes or markup?
    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
checkRd: (-1) power_left_join.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{by}{As in {dplyr}, but extended so user can supply a formula or a list
       |                 ^
checkRd: (-1) power_left_join.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{keep}{A boolean for compatibility with {dplyr}, or a value among "left",
       |                                              ^
checkRd: (-1) preprocess_inputs.Rd:37: Lost braces; missing escapes or markup?
    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'splines2', 'osqp', 'bootnet', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘MplusAutomation’
Packages required but not available:
  'compositions', 'FKSUM', 'simukde', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nasapower’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
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checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'datanugget', 'weights'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rARPACK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘inaparc’

Packages suggested but not available for checking: 'factoextra', 'fclust'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fuzzyjoin’

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

Packages suggested but not available for checking: 'GGally', 'PPtreeViz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘evgam’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'animation', 'ape', 'fields', 'geiger', 'phangorn', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'cvCovEst', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘censable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

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.
checkRd: (-1) ccp_ppm.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
checkRd: (-1) curve_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) gaussian_ppmx.Rd:143: Lost braces; missing escapes or markup?
   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) gaussian_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) ordinal_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) ordinal_ppmx.Rd:147: Lost braces; missing escapes or markup?
   147 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each sujbects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cubature’
Running ‘tinytest.R’ [0s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("ppRep")
  + }
  
  test-estimation.R.............    0 tests    
  test-estimation.R.............    0 tests    Error in library(cubature) : there is no package called 'cubature'
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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.
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘gt’

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', 'shapr', 'PPtreeViz', 'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking: 'ggExtra', 'ggforce'

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: 'reshape2', 'plyr', 'shiny'

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', 'glmnet', '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:
  'emuR', 'gsignal', 'shiny', 'shinyjs', 'soundgen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spdep', 'spatialreg'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'np', 'generalCorr', 'NNS'

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

Packages suggested but not available for checking:
  'plyr', 'Rcpp', 'reshape', 'samplingbook', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mc2d’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'precrec'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_prcr.Rmd’ using rmarkdown

Quitting from lines 19-20 [unnamed-chunk-1] (introduction_to_prcr.Rmd)
Error: processing vignette 'introduction_to_prcr.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘introduction_to_prcr.Rmd’

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

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GiRaF', 'Seurat', 'scater', 'DR.SC', 'ggpubr', 'Rcpp',
  'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'openair', 'raster', 'sf'

Package suggested but not available for checking: ‘spelling’

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

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

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 suggested but not available for checking: 'reticulate', 'spelling'
Running ‘testthat.R’ [67s/45s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(precommit)
  > test_check("precommit")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 13 | PASS 185 ]
  
  ══ Skipped tests (13) ══════════════════════════════════════════════════════════
  • !is_windows() is TRUE (1): 'test-exec.R:23:3'
  • On CRAN (11): 'test-conda.R:207:3', 'test-config.R:15:3',
    'test-impl-hook-roxygenize.R:2:3', 'test-impl-hook-roxygenize.R:46:3',
    'test-impl-hook-roxygenize.R:82:3', 'test-impl-hook-roxygenize.R:95:3',
    'test-impl-hook-roxygenize.R:114:3', 'test-impl-hook-roxygenize.R:127:3',
    'test-impl-hook-roxygenize.R:143:3', 'test-impl-hook-roxygenize.R:155:3',
    'test-zzz.R:2:3'
  • not_conda() is TRUE (1): 'test-impl-hooks-regex-exclude.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-hook-spell-check.R:2:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::map2(path_candidate, path_candidate_temp, hook_state_assert_one, 
      tempdir = tempdir, file_transformer = file_transformer, path_stdout = path_stdout, 
      path_stderr = path_stderr, expect_success = expect_success, 
      std_err = std_err, std_out = std_out, exit_status = exit_status)`: ℹ In index: 1.
  ℹ With name: spell-check-success.md.
  Caused by error:
  ! Expected: No error. Found:
  Error in loadNamespace(x) : there is no package called ‘spelling’
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
  
  [ FAIL 1 | WARN 0 | SKIP 13 | PASS 185 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) diagnose_expressions.Rd:39: Lost braces
    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Peptides’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Packages required but not available: 'shiny', 'DT', 'predhy', 'glmnet'

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: 'ggiraphExtra', 'reshape2', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘MBESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'AER', 'caret', 'crch', 'glmnet', 'lme4', 'plm', 'sampleSelection',
  'survey'
Package suggested but not available for checking: ‘tolerance’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'glmmTMB', 'lme4', 'lmerTest', 'car', 'pbkrtest', 'plotly', 'plyr',
  'splines2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cutpointr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'shiny', 'golem', 'loadeR', 'glmnet', 'traineR', 'shinyjs',
  'shinyAce', 'echarts4r', 'colourpicker', 'shinydashboard',
  'shinycustomloader', 'shinydashboardPlus'

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

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: 'Rcpp', 'RcppArmadillo'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'pROC'

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) preference-package.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:26-27: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'spdep', 'sf', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

Packages suggested but not available for checking:
  'interp', 'glmertree', 'caret', 'pROC', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'justifier', 'openxlsx'
checkRd: (-1) prereg_initialize.Rd:20: Lost braces; missing escapes or markup?
    20 | the (pre)registration form specification (in {preregr} format), see the
       |                                              ^
checkRd: (-1) prereg_initialize.Rd:23: Lost braces; missing escapes or markup?
    23 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
checkRd: (-1) prereg_initialize.Rd:26: Lost braces; missing escapes or markup?
    26 | For an introduction to working with {preregr} (pre)registrations,
       |                                     ^
checkRd: (-1) rmd_templates.Rd:75: Lost braces; missing escapes or markup?
    75 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
checkRd: (-1) rmd_templates.Rd:77: Lost braces; missing escapes or markup?
    77 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
checkRd: (-1) rmd_templates.Rd:81: Lost braces; missing escapes or markup?
    81 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
Running examples in ‘preregr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: source
> ### Title: Programmatically constructing justifier elements
> ### Aliases: source dcsn jstf asrt srce decide decision assert justify
> 
> ### ** Examples
> 
> ### Programmatically create a partial justification object
> exampleAssertion <-
+   preregr::assert(
+     "This is an assertion",
+     source = c(
+       preregr::source('This is a first source'),
+       preregr::source('This is a second source')));
Error in preregr::assert("This is an assertion", source = c(preregr::source("This is a first source"),  : 
  You can't justify without the `justifier` package.
ℹ You can install it with:

install.packages('justifier');
Execution halted
Package required but not available: ‘marelac’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'flextable', 'randomcoloR', 'openxlsx', 'rvg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'gt', 'shinydashboard', 'shinytest'

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

Package suggested but not available for checking: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gdistance', 'ggmap', 'magick', 'raster', 'sf'

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

Packages suggested but not available for checking:
  'miniUI', 'shinyAce', 'shinythemes', 'V8'

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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'plotly'

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

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

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

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'fields', 'sf', 'stars'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape', 'reclin2', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘survey’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cmdstanr', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'bipartite', 'DiagrammeRsvg', 'reshape2', 'rARPACK'
checkRd: (-1) alogistic.Rd:20: Lost braces
    20 | The user does not put these directly into this function, but rather uses code{ode} in the \code{deSolve} package.
       |                                                                              ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ape', 'plyr', 'reshape2'

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.
checkRd: (-1) prim.box.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prim.box.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prim.box.Rd:70: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NesPrInDT.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTAllparts.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulab.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulabAll.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulev.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulevAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTreg.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTregAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) RePrInDT.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
Package suggested but not available for checking: ‘AER’
Packages required but not available:
  'prioritizr', 'terra', 'highs', 'rasterdiv', 'geodiv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'prioritizr', 'terra', 'highs', 'tmap', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) findbeta.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{lower.v}{logical, if TRUE the specified percentile.value is the upper limit for the mean (or the median or the mode) at the specified confidence level (percentile). If {FALSE} the specified percentile.value is the lower limit for the mean (or the median or the mode) at the specified confidence level (percentile). The default is FALSE.}
       |                                                                                                                                                                               ^
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'raster', 'tmap', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'terra', 'raster', 'ape', 'exactextractr', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI', 'highs', 'prioritizrdata', 'fields'

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

Packages suggested but not available for checking: 'pROC', 'ipflasso'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggdist’

Packages suggested but not available for checking:
  'bayesplot', 'brms', 'cmdstanr', 'iwmm', 'philentropy', 'rstan',
  'transport'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘flextable’
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown

Quitting from lines 77-80 [unnamed-chunk-4] (PRISMA.Rmd)
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
there is no package called 'flextable'
--- failed re-building ‘PRISMA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘tm’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘DiagrammeRsvg’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggtext', 'ggpattern', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tune’

Package suggested but not available for checking: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

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

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

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

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.
Package suggested but not available for checking: ‘estimatr’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'keras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bupaR', 'processmapR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bupaR', 'edeaR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'edeaR', 'shiny', 'miniUI', 'plotly', 'Rcpp'

Package suggested but not available for checking: ‘DiagrammeRsvg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bupaR', 'edeaR', 'shiny', 'miniUI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'edeaR', 'reticulate', 'keras', 'tensorflow', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ade4’
Packages required but not available: 'plyr', 'Rcpp'

Package suggested but not available for checking: ‘logcondens’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fmtr', 'reporter'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘AER’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) paasche.Rd:91: Lost braces
    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'DR.SC', 'PRECAST', 'Seurat', 'harmony', 'RcppArmadillo'

Packages suggested but not available for checking: 'scater', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'KrigInv', 'pGPx', 'lhs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RProtoBuf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'DiagrammeRsvg', 'RProtoBuf'
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'qpdf', 'ggrepel'
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'splines2', 'rcpptimer'

Package suggested but not available for checking: ‘rcpptimer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘BayesianTools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) proftools-package.Rd:40: Lost braces
    40 |   by the code{kcachegrind} program available on some operating
       |              ^
Package suggested but not available for checking: ‘shiny’
Packages required but not available: 'pathwayTMB', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcpp’
Packages suggested but not available for checking: 'plyr', 'shiny'
Running examples in ‘progressr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: withProgressShiny
> ### Title: Use Progressr in Shiny Apps: Plug-in Backward-Compatible
> ###   Replacement for shiny::withProgress()
> ### Aliases: withProgressShiny
> 
> ### ** Examples
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Packages required but not available:
  'Rcpp', 'geometry', 'GeneralizedUmatrix', 'shiny', 'shinyjs',
  'shinythemes', 'plotly'

Packages suggested but not available for checking:
  'DataVisualizations', 'spdep', 'fields', 'reshape2', 'Rtsne', 'umap',
  'uwot', 'DatabionicSwarm', 'parallelDist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘EpiEstim’
checkRd: (-1) summary.projections.Rd:33-48: Lost braces
    33 | if (require(incidence)) {
       |                         ^
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'feather', 'reshape', 'plyr', 'qs', 'reticulate'
Packages required but not available:
  'Rcpp', 'rstantools', 'lme4', 'gamm4', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ggrepel', 'rstanarm', 'brms', 'glmnet', 'cmdstanr', 'bayesplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spelling', 'sf'
checkRd: (-1) prolific_prescreener.Rd:254: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_prescreener.Rd:255: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:244: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'ggrepel', 'pcaMethods', 'VIM', 'caret', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggpubr', 'reshape2', 'prophet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'extraDistr', 'rstan', 'rstantools', 'StanHeaders',
  'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'shinyMatrix'
Package suggested but not available for checking: ‘cin’
Package required but not available: ‘car’

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

Packages suggested but not available for checking:
  'shiny', 'shinythemes', 'shinyWidgets', 'shinyjs', 'DT'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'pryr', 'magick', 'shiny'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'narray', 'imputeTS', 'torch', 'greybox'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'rare', 'shiny', 'shinycssloaders', 'shinythemes'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GOSemSim’
Packages required but not available: 'plotly', 'ggrepel'

Packages suggested but not available for checking:
  'shiny', 'r3dmol', 'proDA', 'heatmaply', 'drc', 'STRINGdb', 'iq',
  'ggforce'

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: ‘tokenizers’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rdt’
Packages suggested but not available for checking:
  'transport', 'T4transport'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'AhoCorasickTrie', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘anytime’
Packages required but not available: 'lmomco', 'mev', 'wavScalogram'

Package suggested but not available for checking: ‘GB2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'bigsnpr', 'bigsparser', 'propagate', 'bigparallelr',
  'bigstatsr', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fst’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Morpho’

Package suggested but not available for checking: ‘geomorph’

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: ‘PBImisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘vcr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(PSAWR)
  > 
  > test_check("PSAWR")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PSAWR.Rcheck/tests/testthat/setup-PSAWR.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("PSAWR")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-PSAWR.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'MatchIt', 'optmatch', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'GGally', 'riskRegression', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'cmdstanr', 'flexsurv', 'bayesplot', 'MatchIt', 'BayesPPD', 'gt',
  'gtsummary'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘MatchIt’

Package suggested but not available for checking: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘car’
Running examples in ‘pscl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hurdletest
> ### Title: Testing for the Presence of a Zero Hurdle
> ### Aliases: hurdletest
> ### Keywords: regression
> 
> ### ** Examples
> 
> data("bioChemists", package = "pscl")
> fm <- hurdle(art ~ ., data = bioChemists, dist = "negbin", zero = "negbin")
> hurdletest(fm)
Loading required namespace: car
Failed with error:  ‘there is no package called ‘car’’
Error in hurdletest(fm) : requireNamespace("car") is not TRUE
Calls: hurdletest -> stopifnot
Execution halted
Note: skipping ‘countreg.Rnw’ due to unavailable dependencies: 'car'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'JWileymisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) qpc.Rd:43: Lost braces
    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'qpdf'

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

Package suggested but not available for checking: ‘ggspatial’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'pROC', 'mice', 'mitml', 'lme4', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘forecast’
Error(s) in re-building vignettes:
  ...
--- re-building ‘PSF_vignette.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PSF.Rcheck/vign_test/PSF/vignettes/PSF_vignette_files/figure-html/unnamed-chunk-6-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31420 bytes
Input file size = 31534 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 28614
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 28614

Output IDAT size = 28614 bytes (2806 bytes decrease)
Output file size = 28692 bytes (2842 bytes = 9.01% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PSF.Rcheck/vign_test/PSF/vignettes/PSF_vignette_files/figure-html/unnamed-chunk-7-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 39036 bytes
Input file size = 39162 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 34619
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 34619

Output IDAT size = 34619 bytes (4417 bytes decrease)
Output file size = 34697 bytes (4465 bytes = 11.40% decrease)


Quitting from lines 100-150 [unnamed-chunk-8] (PSF_vignette.Rmd)
Error: processing vignette 'PSF_vignette.Rmd' failed with diagnostics:
there is no package called 'forecast'
--- failed re-building ‘PSF_vignette.Rmd’

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

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

Package suggested but not available for checking: ‘mvnfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) data1.Rd:14: Lost braces
    14 | The data set from {AbouRizk, S.M., Halpin, D.W., Wilson, J. R. (1994). \emph{Fitting beta distributions based on sample data.} Journal of Construction Engineering and Management 120(2), 288–305.}
       |                   ^
checkRd: (-1) data2.Rd:14: Lost braces; missing escapes or markup?
    14 | The data set presents the height of 99 five-year-old British boys in cm downloaded from {http://www.mas.ncl.ac.uk/njnsm/medfac/docs/intro.pdf.}
       |                                                                                         ^
Packages required but not available:
  'intamap', 'gstat', 'automap', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘sf’

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) table1.Rd:14: Lost braces
    14 | The first data set from {Sulewski, P. (2017) \emph{A new test for independence in 2x2 contingency tables,} Acta Universitatis Lodziensis. Folia Oeconomica, 4(330), 55–75}
       |                         ^
checkRd: (-1) table3.Rd:14: Lost braces
    14 | The third data set from {Sulewski, P. (2021). \emph{Logarithmic Minimum Test for Independence in Three Way Con-tingency Table of Small Sizes.} Journal of Statistical Computation and Simulation 91(13), 2780-2799}
       |                         ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bupaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'minqa', 'plm', 'sf', 'spatialreg', 'spdep'

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', 'RcppEigen'

Packages suggested but not available for checking:
  'RcppArmadillo', 'RcppEigen', 'lbfgsb3c', 'lbfgs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'epiR', 'longpower', 'plotly', 'presize', 'pROC', 'shiny',
  'shinycssloaders', 'shinyFeedback', 'shinyhelper'

Packages suggested but not available for checking: 'MESS', 'WebPower'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'np', 'chngpt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rstan', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘misty’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(psycCleaning)
  > 
  > test_check("psycCleaning")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 33 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-centering.R:22:3'): center_group_mean ──────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'misty'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-centering.R:22:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-centering.R:29:3'): z_scored_group_mean ────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'misty'
  Backtrace:
      ▆
   1. ├─... %>% as.numeric() at test-centering.R:29:3
   2. ├─base::scale(., center = TRUE, scale = TRUE)
   3. └─base::loadNamespace(x)
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base (local) withOneRestart(expr, restarts[[1L]])
   6.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 33 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘bib2df’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘effects’
Packages required but not available:
  'qgraph', 'VCA', 'IsingSampler', 'GA', 'Rcpp', 'RcppArmadillo',
  'pbv', 'roptim'

Packages suggested but not available for checking:
  'semPlot', 'graphicalVAR', 'metaSEM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) dprime.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
Packages suggested but not available for checking: 'likert', 'mirt'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'stablelearner', 'mirt'
‘raschtree.Rnw’ using ‘UTF-8’... [7s/8s] NOTE
differences from ‘raschtree.Rout.save’
60,66c60,77
<        V1   
<  Min.   :1  
<  1st Qu.:1  
<  Median :1  
<  Mean   :1  
<  3rd Qu.:1  
<  Max.   :1  
---
> 
> Call:
> raschtree(formula = spisa ~ age + gender + semester + elite + 
>     spon, data = SPISA, minsize = 30)
> 
> Sampler:
> B = 50 
> Method = Subsampling with 63.2% data
> 
> Variable selection overview:
> 
>          freq * mean *
> gender   1.00 1 1.00 1
> spon     0.60 1 0.82 2
> semester 0.18 0 0.18 0
> age      0.04 0 0.04 0
> elite    0.02 0 0.02 0
> (* = original tree)
Note: skipping ‘raschtree.Rnw’ due to unavailable dependencies:
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manual.
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    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
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    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
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    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
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    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
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    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
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Running examples in ‘pulsar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getLamPath
> ### Title: Lambda path
> ### Aliases: getLamPath
> 
> ### ** Examples
> 
> ## Generate the data with huge:
> library(huge)
Error in library(huge) : there is no package called ‘huge’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘other-criteria.Rmd’ using rmarkdown

Quitting from lines 33-60 [unnamed-chunk-2] (other-criteria.Rmd)
Error: processing vignette 'other-criteria.Rmd' failed with diagnostics:
there is no package called 'huge'
--- failed re-building ‘other-criteria.Rmd’

--- re-building ‘pulsar.Rmd’ using rmarkdown
--- finished re-building ‘pulsar.Rmd’

SUMMARY: processing the following file failed:
  ‘other-criteria.Rmd’

Error: Vignette re-building failed.
Execution halted
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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manual.
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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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    72 |   G(u) = (1-r) u  + r Fc_A(Fc_0^{-1}(u))
       |                                 ^
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    62 |   G_A(u) = Fc_A(Fc_0^{-1}(u))
       |                      ^
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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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  'pROC', 'autoimage', 'uwot', 'cdparcoord'

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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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.
Problems with news in ‘NEWS.md’:
No news entries found.
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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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   109 |   \item Van Exel, J., and G. de Graaf, 2005. \emph{Q Methodology: A Sneak Preview}\cr \url{https://qmethodblog.files.wordpress.com/2016/01/qmethodologyasneakpreviewreferenceupdate.pdf}{Available at this link}.
       |                                                                                                                                                                                         ^
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   110 |   \item Brown, S. R., 1980. \emph{Political subjectivity: Applications of Q methodology in political science}, New Haven, CT: Yale University Press.\cr \url{https://qmethodblog.files.wordpress.com/2016/01/brown-1980-politicalsubjectivity.pdf}{Available at this link}.
       |                                                                                                                                                                                                                                                   ^
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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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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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    10 | \item{trueLoc}{A vector of one or more numbers in the set {1, 2, ..., nSubjects} whose locations are to be hidden.}
       |                                                           ^
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    12 | \item{nSubjects}{An integer larger than 1 used to define the set {1, 2, ..., nSubjects}.}
       |                                                                  ^
Packages required but not available: 'shiny', 'shinythemes'

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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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘shinytest2’

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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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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Packages required but not available: 'chromote', 'gutenbergr', 'tidytext'

Package suggested but not available for checking: ‘webshot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'qtl2'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fst', 'qtl2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'qtl2', 'ggrepel'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qtl2', 'qtl2fst', 'fst'

Package suggested but not available for checking: ‘qtl2ggplot’

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: 'devtools', 'qtl2'

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'Rcpp', 'openxlsx', 'glmnet', 'QTL.gCIMapping'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sem', 'pcalg'

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'faraway', 'survminer'
checkRd: (-1) IPWE_mean_IndCen.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
checkRd: (-1) simJLSDdata.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'conquer', 'np', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'mice', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'shinydashboard', 'shinyWidgets'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

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

Package suggested but not available for checking: ‘sphunif’

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

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

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

Packages suggested but not available for checking: 'raster', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

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

Packages suggested but not available for checking: 'tigris', 'tidycensus'

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: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vcr', 'webmockr'
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(qualtRics)
  > 
  > test_check("qualtRics")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/qualtRics.Rcheck/tests/testthat/helper-qualtRics.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("qualtRics")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library(vcr) at tests/testthat/helper-qualtRics.R:2:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Packages suggested but not available for checking: 'GGally', 'DT'
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown

Quitting from lines 92-106 [replication] (wilcox1973.Rmd)
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) cqs.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:37-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:38-41: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

Packages which this enhances but not available for checking:
  'spacyr', 'stm', 'text2vec', 'tidytext', 'tokenizers', 'topicmodels'

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

Packages suggested but not available for checking:
  'quanteda.textplots', 'spelling'

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

Packages suggested but not available for checking:
  'quanteda.textmodels', 'quanteda.textstats', 'spelling', 'wordcloud'

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

Package suggested but not available for checking: ‘spelling’

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:
  'mixtools', 'tclust', 'fmx', 'TukeyGH77'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘np’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘GGally’
Running examples in ‘QuantNorm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: connection.matrix
> ### Title: Construct connection matrix for network analysis
> ### Aliases: connection.matrix
> 
> ### ** Examples
> 
> 
> library(network); library(ggplot2); library(sna); library(GGally) #drawing network graph

‘network’ 1.18.2 (2023-12-04), part of the Statnet Project
* ‘news(package="network")’ for changes since last version
* ‘citation("network")’ for citation information
* ‘https://statnet.org’ for help, support, and other information

Loading required package: statnet.common

Attaching package: ‘statnet.common’

The following objects are masked from ‘package:base’:

    attr, order

sna: Tools for Social Network Analysis
Version 2.8 created on 2024-09-07.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

Error in library(GGally) : there is no package called ‘GGally’
Execution halted
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fda’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'interp', 'conquer'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) quarries.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:26-28: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'TreeTools', 'ape', 'Ternary', 'Rcpp'

Packages suggested but not available for checking: 'phangorn', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘later’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

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: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'str2str', 'plyr', 'car', 'MBESS', 'lme4'

Package suggested but not available for checking: ‘reshape’

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 checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘qpdf’
GNU make is a SystemRequirements.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘terra’

Packages suggested but not available for checking:
  'fastshp', 'raster', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) display_table.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{normtest}{A character indicating test of normality, the default method is \code{\link{shapiro.test}} when sample size no more than 5000, otherwise \code{\link[nortest]{lillie.test}} {Kolmogorov-Smirnov} is used, see package \strong{nortest} for more methods.Use 'shapiro.test', 'lillie.test', 'ad.test', etc to specify methods.}
       |                                                                                                                                                                                             ^
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WRS2’

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

Packages suggested but not available for checking: 'spider', 'adegenet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BayesFactor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘interp’

Package suggested but not available for checking: ‘umap’

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

Packages suggested but not available for checking:
  'shinyBS', 'shinycssloaders', 'shinyFiles', 'shinyjs',
  'shinysurveys', 'shinythemes'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘factoextra’

Packages suggested but not available for checking:
  'baguette', 'viralmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

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: ‘glmnet’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fda.geigen
> ### Title: Generalized Eigen Analysis as in fda Package
> ### Aliases: fda.geigen
> ### Keywords: programming
> 
> ### ** Examples
> 
> library(QZ, quiet = TRUE)
> 
> A <- matrix(as.double(1:6), 2)
> B <- matrix(as.double(c(2, 1, 1, 2)), 2)
> C <- diag(as.double(1:3))
> 
> ret.qz <- fda.geigen(A, B, C)
> 
> ### Verify
> library(fda, quiet = TRUE)
Error in library(fda, quiet = TRUE) : there is no package called ‘fda’
Execution halted
Package required but not available: ‘learnr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘lme4’
checkRd: (-1) do_admb.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_pars.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
Error(s) in re-building vignettes:
  ...
--- re-building ‘R2admb.Rnw’ using knitr

Quitting from lines 523-529 [lme4] (R2admb.Rnw)
Error: processing vignette 'R2admb.Rnw' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘R2admb.Rnw’

SUMMARY: processing the following file failed:
  ‘R2admb.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'interp', 'sf', 'spdep', 'fields'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ReGenesees’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘qpdf’
Packages suggested but not available for checking: 'shiny', 'shinytest'
Package suggested but not available for checking: ‘qpdf’
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘ggrepel’

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

Package suggested but not available for checking: ‘lme4’

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

Package suggested but not available for checking: ‘bootmlm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'reshape'
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) bugs.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:166: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking:
  'caret', 'glmnet', 'ranger'
Packages required but not available: 'shiny', 'DT'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qpdf’
Package required but not available: ‘shiny’

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: 'rmumps', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'RcppXPtrUtils', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qpdf’
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘sf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘r311.Rmd’ using rmarkdown

Quitting from lines 195-198 [unnamed-chunk-14] (r311.Rmd)
Error: processing vignette 'r311.Rmd' failed with diagnostics:
need finite 'ylim' values
--- failed re-building ‘r311.Rmd’

SUMMARY: processing the following file failed:
  ‘r311.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘bio3d’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesianTools', 'sensitivity'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tutorial.helpers’

Packages suggested but not available for checking:
  'gghighlight', 'ggrepel', 'learnr', 'quarto', 'tidymodels'

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: 'ggrepel', 'magick', 'pROC'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'flextable', 'reshape2', 'ggpubr'
checkRd: (-1) r4ss-package.Rd:9: Lost braces; missing escapes or markup?
     9 | A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.19.01, from April 2022).
       |                                                                                                                                                                                                                                                                                                                                                                                                ^
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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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    61 |     \item{\code{H(po_{bm_{n.bm}}, po_act)}:}{ last benchmark prior bm_{n.bm} inducing the fit \code{fits.bm[[n.bm]]} and actual prior}
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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’
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’
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--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown

Quitting from lines 425-461 [twitter_cb_via_BondValuation] (ragtop_convertibles_in_r.Rmd)
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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’
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’
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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.
Problems with news in ‘NEWS.md’:
No news entries found.
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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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--- re-building ‘RankAggreg.Rnw’ using Sweave
Loading required package: cluster
Package 'mclust' version 6.1.1
Type 'citation("mclust")' for citing this R package in publications.

Error: processing vignette 'RankAggreg.Rnw' failed with diagnostics:
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Error in library(kohonen) : there is no package called ‘kohonen’

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Error: Vignette re-building failed.
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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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Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Quitting from lines 34-35 [unnamed-chunk-3] (overview.Rmd)
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SUMMARY: processing the following files failed:
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    18 | where the vector dimension is 2^{response.number}.}
       |                                 ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Running ‘testthat.R’ [1s/1s]
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  Error in library(plumber) : there is no package called 'plumber'
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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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    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
Packages required but not available: 'plyr', 'pander', 'reshape2'

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’
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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’
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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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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’
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’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) S1.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{m_bar}{the sample vector of moments for a specified vector $(h_{a,r},y)$}
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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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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'raster', 'decido', 'rayimage', 'rayvertex', 'spacefillr'

Packages suggested but not available for checking:
  'sf', 'Rvcg', 'rayshader'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'raster', 'terrainmeshr', 'rayimage', 'rayvertex',
  'rayrender', 'RcppArmadillo'

Packages suggested but not available for checking:
  'reshape2', 'magick', 'sf', 'car', 'geosphere', 'terra', 'lidR',
  'elevatr', 'osmdata', 'raybevel'

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

Package suggested but not available for checking: ‘lwgeom’

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

Packages suggested but not available for checking:
  'Rvcg', 'magick', 'raster'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘GPfit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'miniUI', 'shiny'
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'bayesplot', 'RcppEigen',
  'StanHeaders'

Packages suggested but not available for checking: 'rstanarm', 'brms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) rbeta.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rbeta.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rbeta.Rd:35-37: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'geosphere', 'sfheaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggpubr’
Packages required but not available: 'rbi', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'miniUI', 'shiny'
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'ggmcmc', 'GGally', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Packages required but not available: 'plyr', 'Rcpp', 'openxlsx'

Packages suggested but not available for checking: 'ape', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mmrm’

Package suggested but not available for checking: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘imbalance’
Error(s) in re-building vignettes:
  ...
--- re-building ‘booster.Rmd’ using rmarkdown

Quitting from lines 38-56 [unnamed-chunk-2] (booster.Rmd)
Error: processing vignette 'booster.Rmd' failed with diagnostics:
there is no package called 'imbalance'
--- failed re-building ‘booster.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘Rcpp’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘survey’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) R.cache-package.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) R.cache-package.Rd:31-34: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'terra', 'lidR'

Packages suggested but not available for checking:
  'autothresholdr', 'imager', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘interp’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggnetwork', 'ggpubr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘causal_simulation_exemplar.Rmd’ using rmarkdown

Quitting from lines 37-40 [unnamed-chunk-1] (causal_simulation_exemplar.Rmd)
Error: processing vignette 'causal_simulation_exemplar.Rmd' failed with diagnostics:
there is no package called 'ggnetwork'
--- failed re-building ‘causal_simulation_exemplar.Rmd’

--- re-building ‘quick_start.Rmd’ using rmarkdown
--- finished re-building ‘quick_start.Rmd’

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

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

Packages suggested but not available for checking: 'optmatch', 'rrelaxiv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'tidybayes', 'shiny', 'shinythemes',
  'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'rcbalance', 'rlemon'

Packages suggested but not available for checking: 'rrelaxiv', 'optmatch'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'np', 'Benchmarking'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'Rvcg', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘Rcpp’
Running ‘test-all.R’ [5s/6s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(Rcereal)
  > 
  > test_check("Rcereal")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • !Sys.getenv("RCEREAL_TEST_UPDATE") %in% TRUE is TRUE (1):
    'test-update_version.R:21:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-struct.R:10:5'): serialize and deserialize with Rcpp ───────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Rcpp'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-struct.R:10:5
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leaflet', 'plyr', 'oceanmap', 'cleangeo', 'suntools', 'raster',
  'shiny', 'ggedit', 'plotly', 'leaflet.extras2', 'sf'

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', 'pglm', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hdrcde’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rworldmap', 'vcr'
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(rcites)
  > library(tibble)
  > test_check("rcites")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rcites.Rcheck/tests/testthat/setup-rcites.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rcites")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-rcites.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'factoextra', 'FactoMineR', 'mmand', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘outcmaesdisp.dat’
Packages required but not available: 'car', 'readstata13'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'iBBiG', 'BiBitR', 'Rcmdr'

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcmdrMisc', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DoE.wrapper', 'Rcmdr', 'RcmdrMisc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'epiR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'readstata13'

Packages suggested but not available for checking:
  'car', 'meta', 'netmeta', 'plotly', 'pROC', 'tableone', 'lmerTest',
  'rstatix'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcmdrMisc', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'HH', 'Rcmdr'

Packages suggested but not available for checking: 'car', 'latticeExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixlm', 'phia', 'Rcmdr', 'car'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcmdr', 'demography', 'forecast', 'ftsa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

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

Package suggested but not available for checking: ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'Rcmdr', 'latticeExtra'

Packages suggested but not available for checking:
  'ROpenOffice', 'tm.plugin.factiva', 'tm.plugin.lexisnexis',
  'tm.plugin.europresse', 'tm.plugin.alceste'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Package suggested but not available for checking: ‘car’

Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

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

Package suggested but not available for checking: ‘sem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) nonlinearAR1.sim.Rd:8: Lost braces; missing escapes or markup?
     8 | of the form z_n = g(z_{n-1}) + epsilon. A normal distribution is assumed for the innovations.
       |                       ^
Package required but not available: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rcrossref’
Packages required but not available: 'DescTools', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cffr', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘conics’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'reshape2', 'Rcpp', 'gganimate', 'terra', 'lidR', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'shinythemes'
Packages required but not available: 'car', 'survey', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
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: ‘Rcpp’

Package suggested but not available for checking: ‘reticulate’

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: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘MatrixExtra’

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:
  'MomTrunc', 'Rcpp', 'relliptical', 'StempCens', 'RcppArmadillo',
  'roptim'

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

Package suggested but not available for checking: ‘spelling’

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

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: ‘Rcpp’

Package suggested but not available for checking: ‘reticulate’

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 suggested but not available for checking: ‘Rcpp’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppInt64'

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘nanotime’

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', 'RcppBlaze'

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

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

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

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

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

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

Package suggested but not available for checking: ‘RcppEigen’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcpp’
GNU make is a SystemRequirements.
Running ‘doRUnit.R’ [0s/0s]
Running the tests in ‘tests/doRUnit.R’ failed.
Complete output:
  > stopifnot(require(RUnit, quietly = TRUE))
  > stopifnot(require(Rcpp, quietly = TRUE))
  Error: require(Rcpp, quietly = TRUE) is not TRUE
  Execution halted
Packages suggested but not available for checking:
  'RcppArmadillo', 'devtools'
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rcpp.Rcheck/00install.out’ for details.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘RcppMsgPack’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcpp’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RcppThread)
  > 
  > test_check("RcppThread")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('tests.R:6:5'): (code run outside of `test_that()`) ──────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Rcpp'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at tests.R:6:5
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
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: ‘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: ‘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: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'forecast', 'ggmap', 'leaflet', 'leafsync', 'raster', 'terra'

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:
  'crul', 'plyr', 'shiny', 'miniUI', 'DT'

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survminer’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘estimatr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'MatchIt', 'ggpubr', 'PSweight', 'geex', 'BART', 'shiny',
  'shinydashboard', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cellWise’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘tcpl’
Package suggested but not available for checking: ‘Mercator’
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'terra', 'units', 'tidyterra', 'devtools', 'lwgeom', 's2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages suggested but not available for checking: 'shiny', 'evolMap'
Unavailable namespace imported from by a ':::' call: ‘evolMap’
  See the note in ?`:::` about the use of this operator.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'configr', 'semver'

Package suggested but not available for checking: ‘units’

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

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

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'np', 'rdd'

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pander’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages suggested but not available for checking:
  'DT', 'spelling', 'jsonld'
Running examples in ‘rdflib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_rdf
> ### Title: Coerce an object into RDF
> ### Aliases: as_rdf
> 
> ### ** Examples
> 
> as_rdf(mtcars)
Warning in poor_mans_nquads(df, file, ...) :
  prefix not declared, using df:
> as_rdf(list(repo = "rdflib", owner = list("id", "ropensci")))
Error in rdflib::rdf_parse(json2, "jsonld", rdf = rdf) : 
  please install the jsonld package to use this functionality.
Calls: as_rdf -> as_rdf.list -> <Anonymous>
Execution halted
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ADMM', 'CVXR', 'Rcpp', 'RcppDE', 'RSpectra', 'maotai', 'mclustcomp',
  'RcppArmadillo', 'RcppDist'

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

Package suggested but not available for checking: ‘devtools’

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: ‘reshape2’

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'chipPCR', 'reshape2', 'MBmca', 'shiny', 'shinyjs', 'shinythemes',
  'shinyMolBio', 'V8'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rfast', 'Rcpp'

Package suggested but not available for checking: ‘qad’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cellWise’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'urltools', 'glmnet', 'virustotal', 'devtools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'anytime'

Packages suggested but not available for checking: 'survey', 'sspse'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'leaflet', 'devtools', 'OSMscale', 'terra', 'stars', 'shiny'
Packages required but not available: 'stars', 'sf'

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: ‘shiny’

Packages suggested but not available for checking: 'shinytest2', 'spelling'

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

Package suggested but not available for checking: ‘dataui’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'leaflet', 'shiny', 'tippy', 'V8'
Package suggested but not available for checking: ‘shiny’
Running examples in ‘reactCheckbox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: reactCheckboxesInput
> ### Title: Checkbox group input
> ### Aliases: reactCheckboxesInput
> 
> ### ** Examples
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Package suggested but not available for checking: ‘shiny’
Running examples in ‘reactlog-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: reactlog_module_ui
> ### Title: Reactlog Shiny Module
> ### Aliases: reactlog_module_ui reactlog_module_server
> 
> ### ** Examples
> 
> if (!require("shiny")) {
+   message("`shiny` required to run example")
+   return()
+ }
Loading required package: shiny
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘shiny’
`shiny` required to run example
Error: no function to return from, jumping to top level
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(reactlog)
  > 
  > test_check("reactlog")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-shiny_module.R:21:3'): iframe is displayed immediately ─────────
  Error in `value[[3L]](cond)`: unused argument (cond)
  Backtrace:
      ▆
   1. └─reactlog:::test_shiny_version() at test-shiny_module.R:21:3
   2.   └─base::tryCatch(...)
   3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'shiny', 'V8'
Package required but not available: ‘fst’

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: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) reader-package.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:55: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) readMzXmlDir.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'qvalue', 'RcppArmadillo'

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: ‘spelling’
Package required but not available: ‘Rcpp’

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

Package suggested but not available for checking: ‘MatrixExtra’

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: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pdftools', 'streamR', 'striprtf'

Package suggested but not available for checking: ‘quanteda’

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

Packages suggested but not available for checking: 'pool', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘readxl/libs/readxl.so’:
  Found non-API calls to R: ‘Rf_StringFalse’, ‘Rf_StringTrue’

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

See ‘Writing portable packages’ 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: ‘tidyRSS’

Packages suggested but not available for checking: 'devtools', 'zen4R'

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

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 checking math rendering: package 'V8' unavailable
Packages required but not available: 'flextable', 'ggpubr'

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

Package suggested but not available for checking: ‘xpectr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Automotive.Rd:29: Lost braces
    29 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). Own postprocessing.
       |                                                           ^
checkRd: (-1) Automotive.Rd:33: Lost braces
    33 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). 
       |                                                           ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

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

Package suggested but not available for checking: ‘devtools’

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

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

Packages suggested but not available for checking:
  'ddalpha', 'RcppRoll', 'RSpectra', 'splines2'

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:
  'ape', 'picante', 'phangorn', 'phytools'

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

Package suggested but not available for checking: ‘shiny’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'magick', 'opencv', 'sf'
Packages required but not available: 'imager', 'pavo', 'raster'

Package suggested but not available for checking: ‘smoothr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) recombinator.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) recombinator.Rd:35-38: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'MatrixExtra'

Package suggested but not available for checking: ‘recommenderlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recommenderlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recommenderlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recosystem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘survminer’

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: ‘ipred’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘ggpubr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RecordTest.Rmd’ using rmarkdown

Quitting from lines 11-31 [loadLibs] (RecordTest.Rmd)
Error: processing vignette 'RecordTest.Rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building ‘RecordTest.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

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

Packages suggested but not available for checking:
  'prevR', 'fields', 'move', 'move2', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyjs', 'DT', 'colourpicker', 'rintrojs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'splines2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'openxlsx2'

Packages suggested but not available for checking:
  'gt', 'devtools', 'spelling', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'qwraps2'
Running examples in ‘REDCapExporter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_r_data_package
> ### Title: Build R Data Package
> ### Aliases: build_r_data_package build_r_data_package.rcer_rccore
> ###   build_r_data_package.default
> 
> ### ** Examples
> 
> ## Please read the vignette for examples:
> ## vignette(topic = "export", package = "REDCapExporter")
> 
> library(REDCapExporter)
> # avs_raw_core <- export_core()
> data(avs_raw_core)
> tmppth <- tempdir()
> build_r_data_package(avs_raw_core, tmppth, author_roles = list(dewittp = c("cre", "aut")))
Creating source package at /home/hornik/tmp/scratch/RtmpHkvtQ2/rcd14465
Error in loadNamespace(x) : there is no package called ‘devtools’
Calls: build_r_data_package ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘test-as.data.frame.R’ [1s/1s]
  Running ‘test-build_r_pkg.R’ [1s/1s]
  Running ‘test-export.R’ [1s/4s]
  Running ‘test-format_record.R’ [1s/1s]
  Running ‘test-keyring.R’ [0s/1s]
Running the tests in ‘tests/test-build_r_pkg.R’ failed.
Complete output:
  > library(REDCapExporter)
  > temppath <- tempdir()
  > build_r_data_package(
  +   x            = avs_raw_core,
  +   path         = temppath,
  +   author_roles = list(dewittp = c("cre", "aut")),
  + )
  Creating source package at /home/hornik/tmp/scratch/Rtmp3PlzGG/rcd14465
  Error in loadNamespace(x) : there is no package called 'devtools'
  Calls: build_r_data_package ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘api.Rmd’ using rmarkdown

Quitting from lines 26-50 (api.Rmd)
Error: processing vignette 'api.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building ‘api.Rmd’

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

Quitting from lines 18-31 (formatting.Rmd)
Error: processing vignette 'formatting.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building ‘formatting.Rmd’

--- re-building ‘redcap2package.Rmd’ using rmarkdown

Quitting from lines 19-38 (redcap2package.Rmd)
Error: processing vignette 'redcap2package.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building ‘redcap2package.Rmd’

SUMMARY: processing the following files failed:
  ‘api.Rmd’ ‘formatting.Rmd’ ‘redcap2package.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'spelling', 'odbc'
Package suggested but not available for checking: ‘openxlsx2’
Packages required but not available: 'terra', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘REddyProc’

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: ‘PoissonBinomial’

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

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

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

Packages suggested but not available for checking:
  'rmapshaper', 'units', 'RSpectra', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'redist', 'redistmetrics', 'geomander', 'sf', 'censable',
  'tinytiger', 'PL94171', 'alarmdata', 'birdie'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'raster', 'plyr', 'sf', 'terra'

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plumber’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plumber)
  Error in library(plumber) : there is no package called 'plumber'
  Execution halted
Packages required but not available:
  'BAT', 'dismo', 'gdistance', 'geosphere', 'terra', 'predicts'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: REEMtree
> ### Title: Create a RE-EM tree
> ### Aliases: REEMtree
> ### Keywords: tree models
> 
> ### ** Examples
> 
> data(simpleREEMdata)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID)
> 
> # Estimation allowing for autocorrelation
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID,
+ 	correlation=corAR1())
> 
> # Random parameters model for the random effects
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1+X|ID)
> 
> # Estimation with a subset
> sub <- rep(c(rep(TRUE, 10), rep(FALSE, 2)), 50)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID,
+ 	subset=sub)
> 
> # Dataset from the R library "AER"
> data("Grunfeld", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'spdep', 'MCMCglmm'

Package suggested but not available for checking: ‘rcrossref’

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: ‘caret’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Package required but not available: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) make_refreshable.Rd:13: Lost braces
    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fda', 'gamm4', 'lme4', 'RLRsim'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'reshape2', 'lme4', 'plotly', 'refund'

Package suggested but not available for checking: ‘registr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bestglm’

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: 'Rfast', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'shiny', 'shinyjs'

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: 'philentropy', 'terra'

Packages suggested but not available for checking:
  'supercells', 'sf', 'dtwclust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spelling', 'devtools', 'eurostat'
checkRd: (-1) impute_down_nuts.Rd:21: Lost braces
    21 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
checkRd: (-1) validate_data_frame.Rd:19: Lost braces
    19 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘Regional_stats.Rmd’ using rmarkdown

Quitting from lines 18-20 [backrgoundsetup] (Regional_stats.Rmd)
Error: processing vignette 'Regional_stats.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘Regional_stats.Rmd’

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

Quitting from lines 25-28 [setup] (mapping.Rmd)
Error: processing vignette 'mapping.Rmd' failed with diagnostics:
there is no package called 'eurostat'
--- failed re-building ‘mapping.Rmd’

--- re-building ‘recode.Rmd’ using rmarkdown
--- finished re-building ‘recode.Rmd’

--- re-building ‘validation.Rmd’ using rmarkdown
--- finished re-building ‘validation.Rmd’

SUMMARY: processing the following files failed:
  ‘Regional_stats.Rmd’ ‘mapping.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'gamm4', 'lme4', 'RcppArmadillo'

Package suggested but not available for checking: ‘fastglm’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'Rcpp', 'RcppArmadillo'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fbase1.binomial.Rd:32: Lost braces; missing escapes or markup?
    32 | In all base log-likelihood functions, we have dropped any additive terms that are independent of the distribution parameter, e.g. constant terms or those terms that are dependent on the response variable only. This is done for computational efficiency. Therefore, these functions cannot be used to obtain the absolute values of log-likelihood functions but only in the context of optimization and/or sampling. Users can write thin wrappers around these functions to add the constant terms to the function value. (Derivatives do not need correction. For binomial family, all factorial terms are ignored since they only depend on \code{n} and {y}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Packages required but not available:
  'DT', 'shiny', 'golem', 'glmnet', 'loadeR', 'shinyjs', 'traineR',
  'shinyAce', 'echarts4r', 'shinydashboard', 'shinycustomloader',
  'shinydashboardPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘usdm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'GA', 'caret', 'glmnet', 'lbfgs', 'semPlot', 'plyr'

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: 'car', 'glmnet', 'text2vec'

Packages suggested but not available for checking:
  'OpenImageR', 'cdparcoord', 'keras', 'magick', 'partools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ape', 'gap', 'vcfR'
checkRd: (-1) plot.ehh.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}} and \code{\link[graphics]{matplot}}). 
       |                                ^
checkRd: (-1) plot.ehhs.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}}.
       |                                ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘densEstBayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EstimationTools', 'lamW'

Packages suggested but not available for checking: 'autoimage', 'V8'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) rem.dyad.Rd:121: Lost braces; missing escapes or markup?
   121 | \item Single or multiple covariates, time varying: For \code{CovSnd}, \code{CovRec}, or \code{CovInt}, an \code{m} by \code{p} by {n} array whose respective dimensions index time (i.e., event number), covariate, and actor.  For \code{CovEvent}, a \code{m} by \code{p} by \code{n} by \code{n} array, whose dimensions are analogous to the previous case.
       |                                                                                                                                   ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggExtra', 'bde'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘PhaseType’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'relaimpo', 'Rmisc', 'caret', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcmdr’
Packages required but not available: 'Rcpp', 'Ryacas0', 'RcppArmadillo'

Package suggested but not available for checking: ‘ggExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flextable’

Package suggested but not available for checking: ‘pander’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pammtools’

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

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

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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fda’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stream’

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

Packages suggested but not available for checking:
  'devtools', 'reshape2', 'sf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'flextable', 'ggrepel', 'qqplotr', 'ggpubr', 'interactions',
  'openxlsx2', 'Rmisc'
Running examples in ‘rempsyc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nice_normality
> ### Title: Easy normality check per group
> ### Aliases: nice_normality
> ### Keywords: QQ density distribution normality plots
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("ggplot2", quietly = TRUE) && requireNamespace("see", quietly = TRUE) && requireNamespace("patchwork", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ # Make the basic plot
+ nice_normality(
+   data = iris,
+   variable = "Sepal.Length",
+   group = "Species"
+ )
+ 
+ # Further customization
+ nice_normality(
+   data = iris,
+   variable = "Sepal.Length",
+   group = "Species",
+   colours = c(
+     "#00BA38",
+     "#619CFF",
+     "#F8766D"
+   ),
+   groups.labels = c(
+     "(a) Setosa",
+     "(b) Versicolor",
+     "(c) Virginica"
+   ),
+   grid = FALSE,
+   shapiro = TRUE
+ )
+ ## Don't show: 
+ }) # examplesIf
> nice_normality(data = iris, variable = "Sepal.Length", group = "Species")
Error in nice_qq(data = data, variable = variable, group = group, colours = colours,  : 
  The package "qqplotr" (>= 0.0.6) is required for this function.
Calls: <Anonymous> ... eval -> eval -> nice_normality -> nice_qq -> <Anonymous>
Execution halted
Package required but not available: ‘Rcpp’

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: ‘remify’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'lme4', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) rentrez.Rd:17-21: Lost braces
    17 | /enumerated{
       |            ^
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'devtools', 'jsonvalidate', 'miniUI', 'reticulate', 'shiny'
Packages required but not available: 'pool', 'openxlsx'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ddalpha', 'geometry', 'netmeta'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reshape2’

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'PowerTOST', 'lmerTest', 'pbkrtest'

Package suggested but not available for checking: ‘devtools’

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

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: 'flextable', 'lme4', 'lmerTest'

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: ‘shiny’
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
checkRd: (-1) repo_dependencies.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking:
  'devtools', 'ggrepel', 'spelling'
Error(s) in re-building vignettes:
  ...
--- re-building ‘repoRter_nih.Rmd’ using rmarkdown

Quitting from lines 86-93 [unnamed-chunk-5] (repoRter_nih.Rmd)
Error: processing vignette 'repoRter_nih.Rmd' failed with diagnostics:
there is no package called 'ggrepel'
--- failed re-building ‘repoRter_nih.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘fmtr’

Packages suggested but not available for checking: 'survminer', 'libr'

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

Packages suggested but not available for checking:
  'plyr', 'factoextra', 'clusterProfiler', 'enrichplot', 'MetaNet',
  'ggraph', 'rSEA', 'GSVA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesFactor', 'brms', 'ivreg', 'lme4', 'rstanarm'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggpubr', 'pander', 'plyr', 'rstatix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'DT'

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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'miniUI', 'shiny', 'spelling'
Packages required but not available: 'lme4', 'openxlsx', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'geodata', 'qs', 'raster', 'sf', 'terra'
Running examples in ‘reproducible-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gdalProject
> ### Title: 3-Step postProcess sequence for SpatRasters using 'gdalwarp'
> ### Aliases: gdalProject gdalResample gdalMask
> 
> ### ** Examples
> 
> # prepare dummy data -- 3 SpatRasters, 2 SpatVectors
> # need 2 SpatRaster
> rf <- system.file("ex/elev.tif", package = "terra")
> elev1 <- terra::rast(rf)
Error in loadNamespace(x) : there is no package called ‘terra’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘leaflet’

Packages which this enhances but not available for checking:
  'plotly', 'geojsonio'
Package required but not available: ‘urltools’

Package suggested but not available for checking: ‘fiery’

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

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

Package suggested but not available for checking: ‘gganimate’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NCBirths2004.Rd:16: Lost braces
    16 |     \item{\code{Smoker}}{Mother a smoker? code{No}, \code{Yes}}
       |                                               ^
checkRd: (-1) ExpandProbs.Rd:35: Lost braces; missing escapes or markup?
    35 |      {z_probs2 sqrt((n-1)/n) = t_probs,n-1}
       |      ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

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: ‘prospectr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'keras3', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'flextable', 'logKDE', 'reticulate', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Seurat', 'SeuratObject', 'sctransform'
Packages required but not available: 'plyr', 'Rcpp'

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 which this enhances but not available for checking: ‘SmartMeterAnalytics’
Packages required but not available: 'bestNormalize', 'RDP', 'simstudy'

Package suggested but not available for checking: ‘DT’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'geosphere', 'plyr', 'tidybayes'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'marelac', 'roll'

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  'FishResp', 'respirometry'

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: 'terra', 'units'

Package suggested but not available for checking: ‘landscapemetrics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

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

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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Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) harmonize_values.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
Package required but not available: ‘later’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'DT', 'shinydashboard', 'openair'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) elink.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elink.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elink.Rd:74-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reutils-package.Rd:114: Lost braces
   114 |      code{reutils.test.remote} to \code{TRUE} to run the full suite of tests.
       |          ^
Package suggested but not available for checking: ‘rivr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown

Quitting from lines 57-61 [single] (quickstart.Rmd)
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
there is no package called 'rivr'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'bayesplot', 'exdex', 'Rcpp', 'rust', 'RcppArmadillo'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Packages required but not available: 'boot.pval', 'isotree'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'phytools', 'ggtree', 'tidytree', 'treeio', 'reshape',
  'ggimage', 'deeptime'

Package suggested but not available for checking: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DT', 'golem', 'shiny', 'shinycssloaders', 'shinydashboard',
  'shinydashboardPlus', 'shinyjs', 'shinyWidgets'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ape’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ade4', 'plotly', 'shiny', 'shinydashboard', 'tm', 'topicmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rockchalk', 'lme4', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Error(s) in re-building vignettes:
  ...
--- re-building ‘rexer.Rmd’ using rmarkdown

Quitting from lines 113-115 [unnamed-chunk-5] (rexer.Rmd)
Error: processing vignette 'rexer.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘rexer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'leaflet', 'leaflet.extras', 'openxlsx', 'lme4', 'tidytext'
Packages required but not available:
  'Rcpp', 'Rfast', 'Rnanoflann', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CCA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘FSA’
Running examples in ‘RFishBC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aStandard
> ### Title: Finds standard intercept (a) for Fraser-Lee back-calculation
> ###   model for a particular species.
> ### Aliases: aStandard
> ### Keywords: manip
> 
> ### ** Examples
> 
> aStandard("Bluegill")
Error in loadNamespace(x) : there is no package called ‘FSA’
Calls: aStandard ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'sf', 'rworldmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

Package suggested but not available for checking: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'vita'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Package suggested but not available for checking: ‘landscapemetrics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'treemapify', 'xplorerr'

Packages suggested but not available for checking:
  'DT', 'gganimate', 'plotly'

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: 'GEOmap', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'reshape2', 'spelling'
Packages required but not available:
  'Rcpp', 'glmnet', 'pROC', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'hdrcde'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rPref’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'fda', 'plotly', 'shiny', 'Rssa', 'RSpectra', 'rainbow',
  'ftsa', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'permimp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'crul', 'oai'

Packages suggested but not available for checking:
  'terra', 'magick', 'protolite', 'sf', 'vcr'

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.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) tk.browse.Rd:29: Lost braces
    29 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel (see the 'Typing R commands while browsing' section below), the code{TRUE} value is used essentially in the stand alone version.
       |                                                                                                                                                                                                                                                           ^
checkRd: (-1) tk.convert.Rd:17: Lost braces
    17 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel, the code{TRUE} is used essentially in the stand alone version.
       |                                                                                                                                                                                                ^
checkRd: (-1) tk.tracks.Rd:8: Lost braces
     8 |   This function allows to load and edit the \code{\linkS4class{drawable.list}} object that is to be passed to \code{\link{tk.browse}} and code{\link{browsePlot}}, using a Tcl-tk interface
       |                                                                                                                                               ^
Packages required but not available: 'caret', 'ggrepel'

Packages suggested but not available for checking:
  'devtools', 'FactoMineR', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ptw’

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: ‘reticulate’

Packages suggested but not available for checking: 'terra', 'raster'

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

Packages suggested but not available for checking:
  'magick', 'geojsonio', 'sf', 'stars', 'terra', 'leaflet.extras2',
  'spelling', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mapview', 'sf', 'reshape2', 'RefManageR'
Error(s) in re-building vignettes:
  ...
--- re-building ‘precipitation_stochastic_generation_v8.Rmd’ using rmarkdown

Quitting from lines 53-63 [unnamed-chunk-3] (precipitation_stochastic_generation_v8.Rmd)
Error: processing vignette 'precipitation_stochastic_generation_v8.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘precipitation_stochastic_generation_v8.Rmd’

SUMMARY: processing the following file failed:
  ‘precipitation_stochastic_generation_v8.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'crul', 'sf'

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: ‘reticulate’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘servr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DiagrammeRsvg’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_Rgff.Rmd’ using rmarkdown

Quitting from lines 168-176 [unnamed-chunk-11] (Using_Rgff.Rmd)
Error: processing vignette 'Using_Rgff.Rmd' failed with diagnostics:
Packages "DiagrammeRsvg" and "rsvg" are required for exporting a `data.tree::Node` object. Please install them.
--- failed re-building ‘Using_Rgff.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'sf', 'tmap'
checkRd: (-1) Ghana_2021_school_attendance.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Ghana_2021_school_attendance_geometry.Rd:75: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
  ...
--- re-building ‘Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd’ using rmarkdown

Quitting from lines 20-26 [setup] (Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd)
Error: processing vignette 'Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'V8', 'manipulateWidget'
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'magick', 'interp', 'alphashape3d', 'js', 'webshot2', 'shiny',
  'manipulateWidget', 'V8', 'chromote'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'genieclust', 'RSpectra', 'reshape2', 'DescTools',
  'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BDgraph', 'huge', 'pROC', 'reshape2', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) regCVCF.Rd:52: Lost braces; missing escapes or markup?
    52 | a decision tree with {C4.5} on each one. Using each classifier, a prediction of the whole dataset is obtained.
       |                      ^
checkRd: (-1) summary.rfdata.Rd:17: Lost braces; missing escapes or markup?
    17 | A list including information related to the noise filtering process contained in the object \code{object} of class {rfdata} with the following elements:
       |                                                                                                                    ^
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Error(s) in re-building vignettes:
  ...
--- re-building ‘migrate_from_radrowds_us.Rmd’ using rmarkdown

Quitting from lines 65-78 [unnamed-chunk-2] (migrate_from_radrowds_us.Rmd)
Error: processing vignette 'migrate_from_radrowds_us.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘migrate_from_radrowds_us.Rmd’

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

Quitting from lines 64-77 [unnamed-chunk-2] (migrate_from_radwords_ru.Rmd)
Error: processing vignette 'migrate_from_radwords_ru.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘migrate_from_radwords_ru.Rmd’

SUMMARY: processing the following files failed:
  ‘migrate_from_radrowds_us.Rmd’ ‘migrate_from_radwords_ru.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘leaflet’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sf’

Packages suggested but not available for checking: 'geojsonsf', 'terra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'terra', 'sf', 'stars', 'raster'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘bayesm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ade4’

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

Packages suggested but not available for checking: 'stars', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'miniUI'
checkRd: (-1) rhandsontable-package.Rd:8: Lost braces
     8 | R interface for creating tables using Handsontable, url{https://handsontable.com/}
       |                                                        ^
Package required but not available: ‘IHSEP’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shiny.react', 'spelling'

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

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 checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
checkRd: (-1) GenerateClusterData.Rd:34: Lost braces; missing escapes or markup?
    34 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2},
       |                                                ^
checkRd: (-1) GenerateClusterData.Rd:35: Lost braces; missing escapes or markup?
    35 | -v_{(numberOfClusters-1)/2} (if \code{numberOfClusters} is odd)
       |    ^
checkRd: (-1) GenerateClusterData.Rd:36: Lost braces; missing escapes or markup?
    36 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2}
       |                                                ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:25-26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:27-28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:29-30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:31-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:33-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:35-36: Lost braces
    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:37-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:39-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'nonlinearTseries', 'lomb', 'PMCMRplus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘asciicast’
Package required but not available: ‘seqinr’

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

Package suggested but not available for checking: ‘spelling’

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: ‘estimatr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BART', 'twang'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'oro.dicom', 'oro.nifti'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggrepel', 'plotly', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rnaturalearth’

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: 'fst', 'prt'

Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo', 'units', 'pdftools', 'magick'

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

Packages suggested but not available for checking:
  'BAMBI', 'DirStats', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CVXR', 'Rcpp', 'RiemBase', 'Rdimtools', 'T4cluster', 'maotai',
  'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘forecast’
Package required but not available: ‘urltools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
checkRd: (-1) descrip.Rd:122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:129-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:141-144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:145-146: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rigr)
  rigr version 1.0.4: Regression, Inference, and General Data Analysis Tools in R
  > library(car)
  Error in library(car) : there is no package called 'car'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘shiny’

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
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘UpSetR’

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

Packages suggested but not available for checking: 'sf', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survey’
checkRd: (-1) correct_sign.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct_sign.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
Packages suggested but not available for checking: 'fst', 'qs'
Package required but not available: ‘sf’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'relsurv', 'reticulate', 'tune', 'glmnet', 'caret', 'cubature'

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

Package suggested but not available for checking: ‘IsingSampler’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'urltools', 'devtools'

Package suggested but not available for checking: ‘webmockr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       | ^
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |     ^
checkRd: (-1) riskPredict.Rd:38: Lost braces; missing escapes or markup?
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       | ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |     ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                      ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                              ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'mets', 'prodlim', 'Publish', 'ranger', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'glmnet', 'flexsurv', 'hal9001', 'pec', 'penalized', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'nanotime'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
Packages required but not available: 'solrium', 'crul'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘optmatch’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dodgr', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                             ^
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                                                                   ^
Packages required but not available:
  'spam', 'raster', 'sf', 'terra', 'elevatr', 'OCNet', 'Rcpp', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'devtools', 'RSelenium'

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

Package suggested but not available for checking: ‘shiny’

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: 'openxlsx', 'Rcpp'

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

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
License stub is invalid DCF.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ggdemetra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘rjdmarkdown-html.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rjdmarkdown.Rcheck/vign_test/rjdmarkdown/vignettes/rjdmarkdown-html_files/figure-html/unnamed-chunk-3-1.png
2400x1500 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 148014 bytes
Input file size = 148308 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 141598
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 141598

Output IDAT size = 141598 bytes (6416 bytes decrease)
Output file size = 141676 bytes (6632 bytes = 4.47% decrease)


Quitting from lines 47-59 [unnamed-chunk-4] (rjdmarkdown-html.Rmd)
Error: processing vignette 'rjdmarkdown-html.Rmd' failed with diagnostics:
there is no package called 'ggdemetra'
--- failed re-building ‘rjdmarkdown-html.Rmd’

--- re-building ‘rjdmarkdown-pdf.Rmd’ using rmarkdown

Quitting from lines 56-68 [unnamed-chunk-4] (rjdmarkdown-pdf.Rmd)
Error: processing vignette 'rjdmarkdown-pdf.Rmd' failed with diagnostics:
there is no package called 'ggdemetra'
--- failed re-building ‘rjdmarkdown-pdf.Rmd’

SUMMARY: processing the following files failed:
  ‘rjdmarkdown-html.Rmd’ ‘rjdmarkdown-pdf.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggdemetra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘reshape’
Running examples in ‘rjstat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: toJSONstat
> ### Title: Convert data frame(s) to JSON-stat format
> ### Aliases: toJSONstat
> 
> ### ** Examples
> 
> library(reshape)
Error in library(reshape) : there is no package called ‘reshape’
Execution halted
Package required but not available: ‘hunspell’

Package suggested but not available for checking: ‘pdftools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppEigen', 'RcppGSL'

Package suggested but not available for checking: ‘lhs’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'reshape2', 'factoextra', 'FactoMineR', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PTXQC', 'urltools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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.
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

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

Packages suggested but not available for checking:
  'raster', 'stars', 'terra'

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: 'jrc', 'plyr'

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

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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: 'reshape2', 'plyr', 'Rcpp'

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

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

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: 'leaflet', 'raster', 'Rcpp', 'sf'

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: ‘RobustGaSP’

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

Packages suggested but not available for checking:
  'DESeq2', 'DoubletFinder', 'EnhancedVolcano', 'fgsea', 'ggrepel',
  'gprofiler2', 'plotly', 'RcppPlanc', 'Seurat', 'SeuratObject'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httpuv’

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 checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reticulate’

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

Package which this enhances but not available for checking: ‘lmerTest’

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'

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Luminescence', 'shiny', 'shinydashboard', 'RCarb', 'DT'

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

Packages suggested but not available for checking:
  'deeptime', 'devtools', 'ggrepel', 'ggspatial', 'rnaturalearth',
  'rnaturalearthhires', 'palaeoverse', 'units'

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

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

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: 'geojsonsf', 'jsonify', 'sf', 'V8'

Package suggested but not available for checking: ‘units’

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

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: 'plyr', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'katex', 'shiny'
checkRd: (-1) setOption.Matlab.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setOption.Matlab.Rd:40-41: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) ComprehensiveTemperatureGenerator.Rd:68: Lost braces; missing escapes or markup?
    68 | \item{exogen_all}{data frame containing exogenous variable formatted like \code{Tx_all} and {Tn_all}. Default is \code{NULL}. 
       |                                                                                             ^
checkRd: (-1) qqplot_RMAWGEN_Tx.Rd:70: Lost braces; missing escapes or markup?
    70 | \code{Tx_gen},{Tn_gen} and \code{main} must have an even number of elements.
       |               ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ktaucenters’

Package suggested but not available for checking: ‘tclust’

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: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'merTools', 'AICcmodavg', 'ggExtra'
Packages required but not available: 'reshape', 'pander', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking: 'questionr', 'DT'
Running examples in ‘rmdformats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pilltabs
> ### Title: Given a cross-table, outputs HTML code to display several views
> ###   of with a tabbed interface
> ### Aliases: pilltabs
> 
> ### ** Examples
> 
> 
> data(airquality)
> tab <- table(airquality$Month, airquality$Ozone > 25)
> pilltabs(tab)
Error: the questionr package is needed for the pilltabs() function to work. Please install it.
Execution halted
Packages suggested but not available for checking: 'gt', 'tidycmprsk'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'spelling', 'DT'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘OpenMx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘refund’

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

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

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

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’

Package suggested but not available for checking: ‘minqa’

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: ‘plyr’

Package suggested but not available for checking: ‘latticeExtra’

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', 'RcppEigen'

Package suggested but not available for checking: ‘Rmixmod’

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

Packages suggested but not available for checking: 'Rmixmod', 'ClusVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

Packages suggested but not available for checking: 'RMixtCompIO', 'Rmixmod'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RSpectra’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘madshapR’

Package suggested but not available for checking: ‘car’

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

Packages suggested but not available for checking: 'ecr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fPortfolio', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) DO.unit.convert.Rd:24: Lost braces; missing escapes or markup?
    24 |     Units of dissolved oxygen concentration desired, i.e. to be converted to. Must be \code{"mg/L"}, \code{"PP"}, or {"pct"}.
       |                                                                                                                      ^
checkRd: (-1) MR.loops.Rd:80: Lost braces; missing escapes or markup?
    80 | Returns a list of 2. \code{$MR.summary} is of class {data.frame} with 3 columns: \code{$MR} (metabolic rate in user specified units, this is the same as the slope in each linear model), \code{$sd.slope} (standard deviation of slopes calculation), \code{$r.square} (adjusted r square value from each model). This second object is a list of \code{biglm} objects, each one representing a metabolic loop (see McDonnell and Chapman 2016). 
       |                                                     ^
checkRd: (-1) get.pcrit.Rd:27: Lost braces; missing escapes or markup?
    27 | Metabolic rate variable name, formatted as character. Default = \code{NULL}. If this argument takes a value, Pcrit will be calculated by regressing \code{MR.var.name} on \code{DO.var.name}. \code{time.var} and {time.interval} should, in this case, take no value. If \code{MR.var.name} is left as\code{NULL}, then instantaneous metabolic rates (MR) at specified time intervals (see \code{time.interval}) from \code{DO.var.name} and \code{time.var}.
       |                                                                                                                                                                                                                   ^
checkRd: (-1) tot.rss.Rd:35: Lost braces
    35 | code{\link{sumsq}}
       |     ^
checkRd: (-1) tot.rss.Rd:36: Lost braces
    36 | code{\link{get.pcrit}}
       |     ^
Packages required but not available:
  'Rcpp', 'rstan', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'cmdstanr', 'bayesplot', 'mice'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'plotly', 'mice', 'rmsb'
Running examples in ‘rms-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rexVar
> ### Title: rexVar
> ### Aliases: rexVar
> 
> ### ** Examples
> 
> set.seed(1)
> n <- 100
> x1 <- rnorm(n)
> x2 <- rnorm(n)
> x3 <- rnorm(n)
> y  <- x1 + x2 + rnorm(n) / 2.
> d <- data.frame(x1, x2, x3, y)
> dd <- datadist(d); options(datadist='dd')
> f  <- ols(y ~ pol(x1, 2) * pol(x2, 2) + x3,
+           data=d, x=TRUE, y=TRUE)
> plot(anova(f), what='proportion R2', pl=FALSE)
> rexVar(f)

Relative Explained Variation

     x1      x2      x3 x1 * x2 
  0.476   0.508   0.000   0.013 
> g <- bootcov(f, B=20, coef.reps=TRUE)
> rexVar(g, data=d)
Error in loadNamespace(x) : there is no package called ‘rmsb’
Calls: rexVar ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'srlars', 'robStepSplitReg', 'cellWise', 'RcppArmadillo'

Package suggested but not available for checking: ‘mvnfast’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dbscan', 'glmnet', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'bigmemory', 'Rcpp', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

Package suggested but not available for checking: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'mirt', 'TAM'
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
Package required but not available: ‘jsonvalidate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'seqinr', 'reshape2', 'mixtools', 'TopDom', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lhs’

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: 'hot.deck', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DESeq2', 'ggrepel'

Packages suggested but not available for checking: 'apeglm', 'gghighlight'

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

Packages suggested but not available for checking:
  'devtools', 'ggrepel', 'rnaturalearthhires', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package required but not available: ‘fields’

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

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘gaston’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gaston’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Packages required but not available: 'EFA.MRFA', 'fungible'

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

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

Packages suggested but not available for checking:
  'spelling', 'geiger', 'phytools', 'rfigshare', 'knitcitations',
  'xslt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘survey’

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

Packages which this enhances but not available for checking:
  'oro.nifti', 'tractor.base'

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

Package suggested but not available for checking: ‘mmand’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'gemtc', 'ggfittext', 'ggpubr', 'ggrepel', 'heatmaply', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ptw', 'plotly', 'plyr', 'minqa'

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

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

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

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

Package suggested but not available for checking: ‘vcr’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'reshape2', 'shiny'
Running examples in ‘Rnvd3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiBarChart
> ### Title: Multibar chart
> ### Aliases: multiBarChart
> 
> ### ** Examples
> 
> library(Rnvd3)
> # in this example we use the tooltip formatters for styling only; we could
> # achieve the same result with the help of CSS
> dat <- reshape2::melt(
+   apply(HairEyeColor, c(1, 2), sum), value.name = "Count"
+ )
Error in loadNamespace(x) : there is no package called ‘reshape2’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'plyr', 'miniUI', 'shiny'

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

Packages suggested but not available for checking: 'tmap', 'gdistance'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'blockmodels', 'GREMLINS', 'pammtools'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fda', 'GGally', 'robustHD', 'VIM', 'reshape2', 'Rcpp', 'RcppEigen'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fda', 'fda.usc', 'goffda', 'fields'

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: ‘ranger’
Running examples in ‘RobinCar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: robincar_SL
> ### Title: BETA: Covariate adjustment using working models from the super
> ###   learner libraries through the AIPW package with cross-fitting.
> ### Aliases: robincar_SL
> 
> ### ** Examples
> 
> 
> library(SuperLearner)
Loading required package: nnls
Loading required package: gam
Loading required package: splines
Loading required package: foreach
Loaded gam 1.22-5

Super Learner
Version: 2.0-29
Package created on 2024-02-06

> library(ranger)
Error in library(ranger) : there is no package called ‘ranger’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DescTools', 'fdatest', 'spam', 'qpdf'

Package suggested but not available for checking: ‘devtools’

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

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘beadarray’

Package suggested but not available for checking: ‘beadarrayExampleData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘BayesTools’

Packages suggested but not available for checking:
  'metaBMA', 'lme4', 'fixest'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fastGHQuad', 'Rcpp'

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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppDist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'crul', 'RcppSimdJson'

Packages suggested but not available for checking:
  'devtools', 'vcr', 'DiagrammeRsvg', 'sf', 'mapview'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spiderbar’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘GSE’

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', 'RSpectra', 'DescTools', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BayesTools’

Package suggested but not available for checking: ‘flexsurv’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘shiny’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

Package suggested but not available for checking: ‘mvnfast’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) predict.robu.Rd:36-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:43-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:50-55: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘ivreg’

Package suggested but not available for checking: ‘ivgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘PEIP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GGally', 'reshape2'
Note: skipping ‘lmrob_simulation.Rnw’ due to unavailable dependencies:
  'GGally', 'reshape2'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘devtools’

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

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

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

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

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: 'glmnet', 'CVXR'

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

Packages suggested but not available for checking:
  'reshape2', 'rlme', 'lemon', 'robustvarComp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'robreg3S', 'GSE'

Package suggested but not available for checking: ‘systemfit’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘ICS’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'lares', 'prophet', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pROC’
Error(s) in re-building vignettes:
  ...
--- re-building ‘roc-aggregator.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ROCaggregator.Rcheck/vign_test/ROCaggregator/vignettes/roc-aggregator_files/figure-html/visualization-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 12252 bytes
Input file size = 12342 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 9731
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 9731

Output IDAT size = 9731 bytes (2521 bytes decrease)
Output file size = 9809 bytes (2533 bytes = 20.52% decrease)


Quitting from lines 192-238 [appendix-proc] (roc-aggregator.Rmd)
Error: processing vignette 'roc-aggregator.Rmd' failed with diagnostics:
there is no package called 'pROC'
--- failed re-building ‘roc-aggregator.Rmd’

SUMMARY: processing the following file failed:
  ‘roc-aggregator.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘pROC’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'kutils'

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

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

Packages suggested but not available for checking:
  'justifier', 'openxlsx', 'pdftools', 'striprtf'

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
Package required but not available: ‘np’

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: 'reportROC', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fda.usc', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'Rfast', 'TreeDist', 'TreeTools'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘highs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'minqa', 'lbfgsb3c', 'lbfgs'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘osqp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_solve.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'DiagrammeRsvg', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tosca’

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', 'rswipl'

Packages suggested but not available for checking:
  'DiagrammeRsvg', 'rswipl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘magick’

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

Package suggested but not available for checking: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'animation', 'rARPACK'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘imputeTS’

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Packages suggested but not available for checking:
  'rcrossref', 'handlr', 'httpuv', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'caret', 'glmnet', 'keras', 'ranger', 'grf', 'tuneRanger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'ggrepel', 'lme4', 'pander', 'plyr', 'ufs', 'lmerTest'

Packages suggested but not available for checking: 'GGally', 'MBESS'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'plyr', 'raster', 'sf', 'terra'
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                       ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                                  ^
Running examples in ‘rosm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: osm_url_load_async
> ### Title: Load tile URLs
> ### Aliases: osm_url_load_async
> 
> ### ** Examples
> 
> bounds <- wk::rct(
+   252185, 4815826, 739729, 5210280,
+   crs = "EPSG:32620"
+ )
> 
> tiles <- osm_tile_covering(bounds, zoom = 5)
Error in loadNamespace(x) : there is no package called ‘sf’
Calls: osm_tile_covering ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘mrfDepth’

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

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

Package suggested but not available for checking: ‘onion’

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

Packages suggested but not available for checking:
  'MCMCglmm', 'phylobase', 'RNeXML'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ulid’
Package required but not available: ‘graphlayouts’

Package suggested but not available for checking: ‘pagedown’

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: ‘sf’

Package suggested but not available for checking: ‘pagedown’

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.
Package suggested but not available for checking: ‘magick’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘reqres’

Package suggested but not available for checking: ‘fiery’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

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

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: ‘ipmr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'picante', 'bipartite', 'fields', 'geiger', 'mvMORPH',
  'GUniFrac', 'phangorn', 'phytools', 'raster', 'TESS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'RandomFields', 'interp'
checkRd: (-1) Clyde.Rd:8: Lost braces
     8 | These data record the water quality, in terms of dissolved oxygen (\code{DO}) on a percentage scale, at a number of sampling stations (\code{Station}) on the River Clyde.  The date (\code{Day}, \\code{Month}, \code{Year}) is also available, along with the day of the year (\code{Doy} between 1 and 365) and an identified (\code{id}) of the survey on which each measurement was made.
       |                                                                                                                                                                                                         ^
checkRd: (-1) rp.pos.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:31-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:43: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘Seurat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘bio3d’

Package suggested but not available for checking: ‘r3dmol’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ptw’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RPEGLMEN’

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: 'reshape2', 'mirt'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'phytools', 'palaeoverse', 'ggtree', 'ape', 'deeptime', 'sf'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’

Package which this enhances but not available for checking: ‘shiny’
checkRd: (-1) rpivotTable.Rd:60: Lost braces; missing escapes or markup?
    60 | An example is: onRefresh=htmlwidgets::JS("function(config) { Shiny.onInputChange('myPivotData', config); }")
       |                                                            ^
Package required but not available: ‘ecp’

Packages suggested but not available for checking:
  'DT', 'shiny', 'shinyjs', 'shinyWidgets', 'shinycssloaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rbacon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plotImage.blcTree.Rd:17: Lost braces
    17 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) plotImage.glcTree.Rd:16: Lost braces
    16 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) get.poetry.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{output}{Can be any or a combination of the input terms {'author', 'title', 'lines', 'linecount'}. If NULL, all
       |                                                              ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'TDA', 'Mercator'

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

Package suggested but not available for checking: ‘codemetar’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'terra', 'sf', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘imager’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) as.tg.Rd:18: Lost braces; missing escapes or markup?
    18 | Renames the \code{class(tg)["name"]} attribute and sets {class(tg)["type"] <- "TextGrid"} (if it is not already set)
       |                                                         ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DT', 'shiny'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'flexsurv', 'flexsurvcure'
Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rprev)
  Loading required package: survival
  > 
  > test_check("rprev")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 136 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_survival_model.R:80:9'): predict_survival_probability produces correct survival estimates ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'flexsurv'
  Backtrace:
      ▆
   1. ├─rprev (local) test_surv(Surv(time, status) ~ 1, "weibull", data.frame(), time = 500) at test_survival_model.R:93:5
   2. └─base::loadNamespace(x) at test_survival_model.R:80:9
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 136 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mixtools', 'oeli', 'plotROC', '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: 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
Package required but not available: ‘Rcpp’

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

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: 'rpymat', 'reticulate', 'RNifti'

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

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggpmisc', 'pROC', 'GGally'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘servr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GEOmap’

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

Package suggested but not available for checking: ‘shiny’

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

Package suggested but not available for checking: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ex.Rd:20: Lost braces
    20 | Execute a ops-dag using `code{wrap()}` data as values.
       |                              ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                          ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                                                   ^
Packages required but not available: 'lme4', 'phylolm', 'ape', 'phyr'

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.
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Package required but not available: ‘warbleR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Missing or unexported object: ‘RobStatTM::mscale’
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                            ^
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                                        ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                             ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                                         ^
checkRd: (-1) Boost.control.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{n_init}{number of iterations for the SBoost step of RRBoost ($T_{1,max}$) (int)}
       |                                                                       ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                  ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                              ^
Running examples in ‘RRBoost-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Boost
> ### Title: Robust Boosting for regression
> ### Aliases: Boost
> 
> ### ** Examples
> 
> data(airfoil)
> n <- nrow(airfoil)
> n0 <- floor( 0.2 * n )
> set.seed(123)
> idx_test <- sample(n, n0)
> idx_train <- sample((1:n)[-idx_test], floor( 0.6 * n ) )
> idx_val <- (1:n)[ -c(idx_test, idx_train) ]
> xx <- airfoil[, -6]
> yy <- airfoil$y
> xtrain <- xx[ idx_train, ]
> ytrain <- yy[ idx_train ]
> xval <- xx[ idx_val, ]
> yval <- yy[ idx_val ]
> xtest <- xx[ idx_test, ]
> ytest <- yy[ idx_test ]
> model_RRBoost_LADTree = Boost(x_train = xtrain, y_train = ytrain,
+     x_val = xval, y_val = yval, x_test = xtest, y_test = ytest,
+     type = "RRBoost", error = "rmse", y_init = "LADTree",
+     max_depth = 1, niter = 10, ## to keep the running time low
+     control = Boost.control(max_depth_init = 2,
+     min_leaf_size_init = 20, make_prediction =  TRUE,
+     cal_imp = FALSE))
Error: 'mscale' is not an exported object from 'namespace:RobStatTM'
Execution halted
Package suggested but not available for checking: ‘reshape2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘rrcov3way.Rnw’ using Sweave
Robust Methods for Multiway Data Analysis, Applicable also for
Compositional Data (version 0.5-0)


Attaching package: 'rrcov3way'

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

    reorder


Error: processing vignette 'rrcov3way.Rnw' failed with diagnostics:
 chunk 61 (label = amino-excitation) 
Error in library("reshape2") : there is no package called 'reshape2'

--- failed re-building 'rrcov3way.Rnw'

SUMMARY: processing the following file failed:
  'rrcov3way.Rnw'

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'robustHD', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) lateformeeting.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) regrad.Rd:46: Lost braces; missing escapes or markup?
    46 |  \item \code{x-axis} {1st column: The names of the different institutions}
       |                      ^
checkRd: (-1) regrad.Rd:47: Lost braces; missing escapes or markup?
    47 |  \item \code{y-axis} {2nd column: The value to show completeness}
       |                      ^
Packages required but not available: 'lhs', 'sensitivity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flextable’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'bayesm', 'rrpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘biwavelet’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'Rcpp', 'RcppArmadillo'

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

Packages suggested but not available for checking:
  'phangorn', 'car', 'picante', 'ddpcr', 'geomorph', 'pdftools',
  'mvMORPH', 'qpdf', 'Rvcg', 'Morpho', 'evolqg', 'Rphylopars',
  'phylolm', 'webshot2'

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

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

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: 'Rcpp', 'plotly', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘reshape2’
'LazyData' is specified without a 'data' directory
Note: skipping ‘ragged.Rmd’ due to unavailable dependencies: 'reshape2'
Note: skipping ‘rescaling_data.Rmd’ due to unavailable dependencies:
  'reshape2'
Packages required but not available:
  'flextable', 'rvg', 'shiny', 'editData', 'shinyWidgets', 'ggpubr',
  'ztable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'simcdm', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggpubr’

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

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

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

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘recipes’
Package required but not available: ‘plyr’

Packages suggested but not available for checking: 'fields', 'qgraph'

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

Packages suggested but not available for checking:
  'fields', 'qgraph', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leafem', 'leaflet', 'tmap', 'fields', 'calendR', 'sf', 'stars',
  'terra', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
checkRd: (-1) rSCA.modeling.Rd:61: Lost braces; missing escapes or markup?
    61 |                 a predefined string to specify how the information of leaf nodes will be stored in the map file. A full list of options for mapvalue is: {mean, max, min, median, interval, radius, variation, random}. Default value is "mean". Use "interval" to get an interval bounded by the minimum and maximum values, (i.e., [min, max]). The option of "radius" will output the mean and the radius [i.e., (max - min) / 2] at the same time. Use "variation" to output the mean and the standard deviation. The option of "random" will output the information as an interval like the "interval" option, but it will use a random value within the interval as the predicted value.
       |                                                                                                                                                          ^
Packages required but not available: 'shiny', 'shinycssloaders', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

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

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

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:
  'plumber', 'quarto', 'reticulate', 'shiny'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape', 'glmnet', 'FactoMineR', 'princurve', 'randomcoloR',
  'umap', 'plotly', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggraph', 'ggimage'
Running examples in ‘rSDI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSDI
> ### Title: plotSDI generates a plot of the network and SDI metrics on a
> ###   geographic map.
> ### Aliases: plotSDI
> 
> ### ** Examples
> 
> TMSDI <- SDI(TurkiyeMigration.flows, TurkiyeMigration.nodes, variant="vuw")
> plotSDI(TMSDI, variant="vuw", circle.size.scale=1)
Error in plotSDI(TMSDI, variant = "vuw", circle.size.scale = 1) : 
  ggraph is required
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rSDI.Rmd’ using rmarkdown

Quitting from lines 54-73 [unnamed-chunk-3] (rSDI.Rmd)
Error: processing vignette 'rSDI.Rmd' failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘rSDI.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'shiny', 'shinyWidgets', 'keys'

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: ‘hommel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GEOmap’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘wdman’

Package suggested but not available for checking: ‘binman’

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.
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘ggraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Categorical-and-continuous-features.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (Categorical-and-continuous-features.Rmd)
Error: processing vignette 'Categorical-and-continuous-features.Rmd' failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘Categorical-and-continuous-features.Rmd’

--- re-building ‘separate-peels-quintet.Rmd’ using rmarkdown

Quitting from lines 28-35 [unnamed-chunk-2] (separate-peels-quintet.Rmd)
Error: processing vignette 'separate-peels-quintet.Rmd' failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘separate-peels-quintet.Rmd’

SUMMARY: processing the following files failed:
  ‘Categorical-and-continuous-features.Rmd’
  ‘separate-peels-quintet.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'flextable', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'rstpm2'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rstac', 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plyr', 'tokenizers'

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: ‘gurobi’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘Vdgraph’
Unknown package ‘Vdgraph’ in Rd xrefs
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘NeuralNetTools’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'kohonen', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'geosphere', 'tigris', 'raster', 'plyr'

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

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

Packages suggested but not available for checking:
  'INLA', 'RSpectra', 'inlabru', 'scoringRules'

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', 'RcppEigen'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DT', 'MVN', 'ShinyItemAnalysis', 'gt', 'mirt', 'plyr', 'semPlot',
  'shinyBS', 'shinyWidgets', 'shinycustomloader', 'shinyjs',
  'shinythemes', 'shiny'

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

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

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

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

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

Packages suggested but not available for checking: 'RSpectra', 'PRIMME'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'tmap', 'leaflet', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'bayesplot', 'lme4', 'rstan', 'rstantools', 'shinystan',
  'StanHeaders', 'RcppEigen'

Packages suggested but not available for checking:
  'StanHeaders', 'gamm4', 'shiny', 'V8'

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

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

Package suggested but not available for checking: ‘spelling’

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

Packages suggested but not available for checking:
  'shinystan', 'bayesplot', 'rstantools', 'V8'

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

Package suggested but not available for checking: ‘rstan’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'sf', 'terra', 'reshape2', 'exactextractr', 'Rcpp',
  'RcppArmadillo'

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

Packages suggested but not available for checking:
  'readstata13', 'survPen', 'flexsurv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geosphere', 'ggspatial', 'googleway', 'maptiles', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'epiR', 'mc2d'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bellreg’

Packages suggested but not available for checking:
  'flexsurv', 'frailtyEM', 'GGally', 'LambertW', 'survstan'

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: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'magick', 'spelling'
Running examples in ‘rsvg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rsvg
> ### Title: Render SVG into Bitmap
> ### Aliases: rsvg rsvg_raw rsvg_nativeraster rsvg_webp rsvg_png rsvg_pdf
> ###   rsvg_svg rsvg_ps rsvg_eps
> 
> ### ** Examples
> 
> # create some svg
> options(example.ask=FALSE)
> tmp <- tempfile()
> svglite::svglite(tmp, width = 10, height = 7)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = factor(cyl))
Warning: `qplot()` was deprecated in ggplot2 3.4.0.
> dev.off()
pdf 
  2 
> 
> # convert directly into a vector or bitmap graphics format
> rsvg_pdf(tmp, "out.pdf")
> rsvg_png(tmp, "out.png")
> rsvg_svg(tmp, "out.svg")
> rsvg_ps(tmp, "out.ps")
> rsvg_eps(tmp, "out.eps")
> 
> # render into raw bitmap array
> bitmap <- rsvg(tmp, height = 1440)
> dim(bitmap) # h*w*c
[1] 1440 2057    4
> 
> # render to native raster object
> nr <- rsvg_nativeraster(tmp)
> # grid::grid.raster(nr)
> 
> # read in your package of choice
> magick::image_read(bitmap)
Error in loadNamespace(x) : there is no package called ‘magick’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘svg-css.Rmd’ using rmarkdown

Quitting from lines 91-92 [unnamed-chunk-8] (svg-css.Rmd)
Error: processing vignette 'svg-css.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building ‘svg-css.Rmd’

SUMMARY: processing the following file failed:
  ‘svg-css.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘out.eps’ ‘out.pdf’ ‘out.png’ ‘out.ps’ ‘out.svg’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Package suggested but not available for checking: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tokenbrowser’

Package which this enhances but not available for checking: ‘spacyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'car', 'flextable'
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phytools', 'ape', 'distory', 'paco'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcppMsgPack', 'urltools'

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

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:
  'tm', 'FactoMineR', 'explor', 'wordcloud', 'tm.plugin.factiva',
  'tm.plugin.lexisnexis', 'tm.plugin.europresse', 'tm.plugin.alceste'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DT’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rNOMADS’
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'tm', 'ipred', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
checkRd: (-1) tw_options.Rd:22: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'DescTools', 'interactions', 'lme4', 'plyr'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'extraDistr', 'reshape2', 'JuliaCall', 'qpdf'

Package suggested but not available for checking: ‘Gviz’

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: ‘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: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'timetk', 'tsibble', 'Rcpp'

Packages suggested but not available for checking:
  'rugarch', 'tidyquant', 'feasts', 'fabletools', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘hexSticker’
Packages required but not available:
  'caret', 'lidR', 'keras', 'reticulate', 'sf', 'tensorflow'

Package suggested but not available for checking: ‘terra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Ryacas’

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: ‘vcr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(rtoot)
  > 
  > test_check("rtoot")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rtoot.Rcheck/tests/testthat/setup-rtoot.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("rtoot")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-rtoot.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Packages required but not available: 'gstat', 'sf', 'units'

Packages suggested but not available for checking: 'intamap', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'ggrepel'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lmerTest', 'reshape2'

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

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.
checkRd: (-1) rt_GET.Rd:13: Lost braces
    13 | code{\link[httr]{GET}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
checkRd: (-1) rt_POST.Rd:13: Lost braces
    13 | code{\link[httr]{POST}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
Packages suggested but not available for checking:
  'ggrepel', 'leaflet', 'leaflet.extras'
Packages required but not available:
  'Rcpp', 'terra', 'plyr', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘geometry’
Running ‘attributes.R’ [0s/0s]
  Comparing ‘attributes.Rout’ to ‘attributes.Rout.save’ ... OK
  Running ‘basic.R’ [0s/0s]
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ... OK
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("RTriangle")
  Loading required package: RTriangle
  [ FAIL 2 | WARN 1 | SKIP 2 | PASS 10 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • empty test (2): 'test-triangulate.R:46:1', 'test-triangulate.R:85:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-triangulate.R:16:3'): triangulate can trianglulate a square ────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'geometry'
  Backtrace:
      ▆
   1. ├─RTriangle (local) tri.area(tp$P, tp$T) at test-triangulate.R:16:3
   2. └─base::loadNamespace(x) at test-triangulate.R:9:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-triangulate.R:31:3'): triangulate can trianglulate an object with a concavity subject to a minimum area constraint ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'geometry'
  Backtrace:
      ▆
   1. ├─RTriangle (local) tri.area(tp$P, tp$T) at test-triangulate.R:31:3
   2. └─base::loadNamespace(x) at test-triangulate.R:9:3
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 1 | SKIP 2 | PASS 10 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

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

Package suggested but not available for checking: ‘cmdstanr’

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

Package suggested but not available for checking: ‘gsDesign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘anytime’

Package suggested but not available for checking: ‘RQuantLib’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'texmex', 'tsibble'

Packages suggested but not available for checking: 'rnaturalearth', 'terra'

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: 'terra', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spelling', 'vcr'
Problems with news in ‘NEWS.md’:
No news entries found.
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  > library(RTTWebClient)
  > test_check("RTTWebClient")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RTTWebClient.Rcheck/tests/testthat/setup-RTTWebClient.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("RTTWebClient")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-RTTWebClient.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Package suggested but not available for checking: ‘vcr’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(Rtumblr)
  > 
  > test_check("Rtumblr")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rtumblr.Rcheck/tests/testthat/setup-Rtumblr.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("Rtumblr")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-Rtumblr.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Found the following files/directories:
  ‘Tsttwalk.dat’
Packages suggested but not available for checking:
  'httpuv', 'magick', 'spelling', 'vcr'
Packages required but not available:
  'colourvalues', 'Rcpp', 'RcppSimdJson', 'geometry'

Packages suggested but not available for checking:
  'ggpmisc', 'ggpubr', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                   ^
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                                    ^
Packages suggested but not available for checking:
  'C50', 'Cubist', 'recipes', 'spelling', 'xrf'
Package required but not available: ‘roll’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'flextable', 'formods', 'onbrand', 'plotly', 'shiny',
  'shinyAce', 'shinyWidgets', 'rxode2'

Packages suggested but not available for checking:
  'nlmixr2lib', 'nonmem2rx', 'prompter', 'rxode2et', 'shinydashboard',
  'ubiquity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gtsummary', 'quarto', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fda', 'refund'
Running examples in ‘runDRT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_drt
> ### Title: Run Doubly Ranked Tests
> ### Aliases: run_drt run_drt.default run_drt.formula
> 
> ### ** Examples
> 
> #### Two Sample Problem: Resin Viscosity ####
> library(FDboost)
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
This is FDboost 1.1-2. 
> data("viscosity")
> 
> Xv    <- matrix(viscosity$visAll, nrow = nrow(viscosity$visAll), ncol = ncol(viscosity$visAll))
> fXv   <- refund::fpca.face(Xv)
Error in loadNamespace(x) : there is no package called ‘refund’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'greta', 'tensorflow', 'ggmcmc', 'rstan'
'library' or 'require' calls in package code:
  ‘nimble’ ‘nimbleAPT’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' 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: ‘urltools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggforce', 'reshape2', 'shiny'

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: 'bang', 'revdbayes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'shiny', 'colourpicker'
checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
Packages required but not available: 'ade4', 'car', 'FactoMineR', 'lme4'

Packages suggested but not available for checking:
  'ape', 'FSA', 'glmmTMB', 'labdsv', 'mixOmics', 'RGCCA'

Package which this enhances but not available for checking: ‘glmmADMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                ^
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                                   ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'clusterProfiler', 'ggpubr', 'plotly'

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

Package suggested but not available for checking: ‘Morpho’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggdist’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'chromote', 'spelling'
Packages required but not available: 'Rcpp', 'gdtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gpuR’
Packages required but not available: 'kde1d', 'Rcpp', 'RcppEigen', 'wdm'

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'Rcpp', 'Rfast', 'scModels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'plotly', 'shiny'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘imager’
checkRd: (-1) HardThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
checkRd: (-1) SoftThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gt', 'phonics', 'RecordLinkage', 'sf'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'pryr', 'arm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘marked’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'raster', 'units'

Packages suggested but not available for checking: 'geosphere', 'lwgeom'

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: 'meteor', 'Rcpp'

Packages suggested but not available for checking: 'terra', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BiocPkgTools', 'reticulate'
Package unavailable to check Rd xrefs: ‘BiocPkgTools’
Packages required but not available: 'fields', 'raster', 'terra'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rworldmap’
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘findR’
Packages required but not available: 'geosphere', 'reshape2'

Packages suggested but not available for checking:
  'bfast', 'spelling', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'reshape2', 'phangorn', 'plyr', 'GGally'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rxode2ll', 'qs', 'sitmo', 'RcppArmadillo', 'RcppEigen',
  'StanHeaders'

Packages suggested but not available for checking:
  'DT', 'ggrepel', 'learnr', 'shiny', 'symengine', 'xgxr', 'units',
  'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.eff.ridge.Rd:6: Lost braces
     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
Package required but not available: ‘Rcpp’

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

Package suggested but not available for checking: ‘devtools’

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plyr', 'reshape2'

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

Packages suggested but not available for checking:
  'car', 'metan', 'devtools', 'spelling'

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: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ciReg.Rd:10: Lost braces
    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
Packages required but not available:
  'bigmemory', 'ClimProjDiags', 'plyr', 'multiApply',
  'SpecsVerification', 'easyVerification'

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: ‘glmnet’

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: ‘paws.storage’

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

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

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘DDD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘GUILDS’

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

Package suggested but not available for checking: ‘sae’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sae’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘CARBayesdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sae’

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: 'Rcpp', 'spdep', 'RcppArmadillo'

Packages suggested but not available for checking: 'sae', 'saeSim'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'emdi', 'openxlsx', 'reshape2', 'HLMdiag'

Packages suggested but not available for checking: 'simFrame', 'sf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘torch’
Packages required but not available: 'DT', 'plotly', 'shiny', 'Tendril'

Packages suggested but not available for checking:
  'shinytest', 'safetyGraphics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'datamods', 'rclipboard', 'safetyCharts', 'shiny', 'shinyjs',
  'sortable'

Packages suggested but not available for checking:
  'shinydashboard', 'shinytest', 'listviewer', 'shinybusy',
  'shinyWidgets'

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

Package suggested but not available for checking: ‘vote’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'learnr', 'spelling', 'PMCMRplus', 'devtools', 'DescTools', 'GGally',
  'car', 'ggiraphExtra', 'FactoMineR', 'caret'
Running examples in ‘sageR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: air_pollution
> ### Title: Air pollution data
> ### Aliases: air_pollution
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(air_pollution)
> str(air_pollution)
'data.frame':	50 obs. of  15 variables:
 $ CITY   : Factor w/ 49 levels "AUGUSTA","AUSTIN",..: 38 25 27 26 23 15 14 39 45 21 ...
 $ TMR    : int  1096 789 1072 1199 967 950 841 1113 1031 845 ...
 $ SMIN   : int  30 29 88 155 60 31 2 50 67 18 ...
 $ SMEAN  : int  163 70 123 229 70 88 61 94 86 34 ...
 $ SMAX   : int  349 161 245 340 137 188 188 186 309 198 ...
 $ PMIN   : int  56 27 70 63 56 61 54 34 52 45 ...
 $ PMEAN  : int  119 74 166 147 122 183 126 120 104 119 ...
 $ PMAX   : int  223 124 452 253 219 329 229 242 193 304 ...
 $ PM2    : num  116.1 21.3 15.8 1357.2 18.1 ...
 $ PERWH  : num  97.9 60 98.7 93.1 97 95.9 95.8 98.2 90.5 92.5 ...
 $ NONPOOR: num  83.9 69.1 73.3 87.3 73.2 87.1 86.9 86.1 86.1 78.5 ...
 $ GE65   : int  109 64 103 103 93 97 82 112 98 81 ...
 $ LPOP   : num  5.86 5.27 5.45 5.79 5.41 ...
 $ l_pm2  : num  4.75 3.06 2.76 7.21 2.9 ...
 $ l_pmax : num  5.41 4.82 6.11 5.53 5.39 ...
> library(ggplot2)
> library(GGally)
Error in library(GGally) : there is no package called ‘GGally’
Execution halted
Packages required but not available:
  'Rcpp', 'lowmemtkmeans', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘glmnet’
Running examples in ‘sAIC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sAIC
> ### Title: Compute the Akaike information criterion for the lasso in
> ###   generalized linear models
> ### Aliases: sAIC
> ### Keywords: models regression
> 
> ### ** Examples
> 
> library(MASS)
> library(glmnet)
Error in library(glmnet) : there is no package called ‘glmnet’
Execution halted
Packages required but not available: 'caret', 'terra'

Package suggested but not available for checking: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘anytime’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘collapse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smotefamily', 'ranger', 'pROC'

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

Package suggested but not available for checking: ‘gdistance’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'boot.pval', 'reshape2', 'survey', 'svrep'

Package suggested but not available for checking: ‘jtools’

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.
Package required but not available: ‘systemfit’

Package suggested but not available for checking: ‘Ecdat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘DescTools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘samplesizeCMH-introduction.Rmd’ using rmarkdown

Quitting from lines 136-139 [BreslowDay] (samplesizeCMH-introduction.Rmd)
Error: processing vignette 'samplesizeCMH-introduction.Rmd' failed with diagnostics:
there is no package called 'DescTools'
--- failed re-building ‘samplesizeCMH-introduction.Rmd’

--- re-building ‘samplesizeCMH-power.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/samplesizeCMH.Rcheck/vign_test/samplesizeCMH/vignettes/samplesizeCMH-power_files/figure-html/contraceptives-plot-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19329 bytes
Input file size = 19431 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15462
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15462

Output IDAT size = 15462 bytes (3867 bytes decrease)
Output file size = 15540 bytes (3891 bytes = 20.02% decrease)

--- finished re-building ‘samplesizeCMH-power.Rmd’

--- re-building ‘samplesizeCMH-samplesize.Rmd’ using rmarkdown
--- finished re-building ‘samplesizeCMH-samplesize.Rmd’

SUMMARY: processing the following file failed:
  ‘samplesizeCMH-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Note: skipping ‘my-vignette.Rnw’ due to unavailable dependencies: 'lme4'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'lme4', 'RcppArmadillo', 'RcppDist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RBesT’

Package suggested but not available for checking: ‘rstanarm’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MSEtool', 'TMB', 'RcppEigen'

Packages suggested but not available for checking:
  'caret', 'extraDistr', 'Gmisc', 'reshape2', 'shiny', 'tmbstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BART’

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: ‘RLumModel’

Packages suggested but not available for checking:
  'EMMAgeo', 'Luminescence'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ape', 'blockmodels', 'car', 'huge', 'networkTomography', 'ngspatial'
Packages suggested but not available for checking:
  'AER', 'car', 'lme4', 'plm'
Note: skipping ‘sandwich-CL.Rnw’ due to unavailable dependencies: 'plm'
Note: skipping ‘sandwich-OOP.Rnw’ due to unavailable dependencies: 'AER'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggtext', 'odbc'

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

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:
  'shiny', 'colourpicker', 'manipulateWidget', 'DT'
Error(s) in re-building vignettes:
  ...
--- re-building ‘sankeywheel.Rmd’ using rmarkdown

Quitting from lines 43-44 [unnamed-chunk-3] (sankeywheel.Rmd)
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘sankeywheel.Rmd’

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

Error: Vignette re-building failed.
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:
  'plyr', 'pcaMethods', 'reshape2', 'shiny', 'DT'

Package suggested but not available for checking: ‘pander’

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

Package suggested but not available for checking: ‘units’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'widyr', 'tidytext', 'ggraph', 'reshape2', 'ldatuning', 'topicmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘openair’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘terra’

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

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'srvyr', 'qs', 'quarto', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [31s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(saros.base)
  > 
  > testthat::test_check("saros.base")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 279 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ungroup_data.R:5:3'): ungroup_data ─────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'srvyr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-ungroup_data.R:5:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 279 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘ggiraph’

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

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

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘openxlsx’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'shiny', 'smacof'
Package required but not available: ‘reticulate’

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: ‘spelling’
Package required but not available: ‘AICcmodavg’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Usinglmer.Rnw’ using Sweave

Error: processing vignette 'Usinglmer.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library(lme4) : there is no package called ‘lme4’

--- failed re-building ‘Usinglmer.Rnw’

SUMMARY: processing the following file failed:
  ‘Usinglmer.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
GNU make is a SystemRequirements.
Packages required but not available: 'fmtr', 'libr', 'reporter', 'procs'

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

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

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘geosphere’

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

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘etm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'MSGARCH', 'forecast', 'rugarch'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'blockmodels', 'Rcpp', 'GREMLINS', 'reshape2', 'prodlim',
  'RcppArmadillo'

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

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: ‘reshape2’

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: ‘Rcpp’

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: ‘sf’
Packages which this enhances but not available for checking:
  'gurobi', 'pogs', 'osqp'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reticulate’

Package suggested but not available for checking: ‘tensorflow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
License stub is invalid DCF.
Package suggested but not available for checking: ‘TAM’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'Seurat', 'harmony', 'SeuratObject'

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

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

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

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Seurat', 'SeuratObject'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Packages suggested but not available for checking:
  'leafem', 'leaflet', 'leafpop', 'mapview', 'raster', 'spelling'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) get.events.Rd:51: Lost braces
    51 |   code{\link[deSolve]{events}}
       |       ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggstance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘shiny’
checkRd: (-1) scatterD3.Rd:209: Lost braces; missing escapes or markup?
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
checkRd: (-1) scatterD3.Rd:209: Lost braces
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'DataVisualizations', 'ggExtra', 'plotly', 'FCPS', 'parallelDist',
  'secr', 'ClusterR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
checkRd: (-1) PermBiclust.beta.ks.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:30: Lost braces
    30 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust.Rd:33: Lost braces
    33 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:36: Lost braces
    36 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sparseMatrixStats', 'spam'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

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

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

Package suggested but not available for checking: ‘pcalg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggrepel', 'pROC', 'Rcpp', 'uwot', 'RcppArmadillo', 'RcppEigen'

Package suggested but not available for checking: ‘rmumps’

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: 'Seurat', 'ggrepel', 'SeuratObject'

Packages suggested but not available for checking:
  'dittoSeq', 'DropletUtils', 'ggpubr', 'Nebulosa', 'reticulate',
  'rliger', 'scuttle', 'qs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatialreg', 'spdep', 'sf', 'ggspatial'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'odbc', 'spelling'
Packages required but not available:
  'Seurat', 'harmony', 'NMF', 'reshape2', 'glmGamPoi'

Packages suggested but not available for checking:
  'reticulate', 'plotly', 'DESeq2', 'scater', 'scran', 'sctransform',
  'Linnorm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'uwot', 'Rcpp', 'RcppAnnoy', 'torch', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'plyr', 'shiny', 'shinytest', 'rclipboard'
Package required but not available: ‘Seurat’

Packages suggested but not available for checking:
  'DT', 'GOSemSim', 'ontoProc', 'plotly', 'rrvgo', 'spelling', 'shiny',
  'shinythemes', 'shinyWidgets', 'SingleCellSignalR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'mmints', 'shiny', 'shinythemes'

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

Packages suggested but not available for checking: 'scater', 'splatter'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Seurat’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'apcluster', 'OpenImageR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggraph’

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ez’
checkRd: (-1) schoRsch.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:45: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘tidytext’
Error(s) in re-building vignettes:
  ...
--- re-building ‘theoffice.Rmd’ using rmarkdown

Quitting from lines 52-54 [unnamed-chunk-5] (theoffice.Rmd)
Error: processing vignette 'theoffice.Rmd' failed with diagnostics:
there is no package called 'tidytext'
--- failed re-building ‘theoffice.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggtext', 'hexSticker', 'hrbrthemes'
Running examples in ‘schtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_lucas
> ### Title: Sarah's go-to theme for ggplot2
> ### Aliases: theme_lucas
> 
> ### ** Examples
> 
> library(ggplot2)
> library(showtext)
Loading required package: sysfonts
Loading required package: showtextdb
> 
> # run once to download the PT Sans fonts
> font_add_google(name = "PT Sans", family = "PT Sans")
> font_add_google(name = "PT Sans Narrow", family = "PT Sans Narrow")
> showtext_auto()
> 
> # make a plot with theme_lucas()
> ggplot(mtcars) +
+   aes(x = mpg, y = wt, color = cyl) +
+   geom_point() +
+   theme_lucas()
Error in loadNamespace(x) : there is no package called ‘hrbrthemes’
Calls: theme_lucas ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(schtools)
  > 
  > test_check("schtools")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 49 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plot.R:11:1'): (code run outside of `test_that()`) ─────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'hrbrthemes'
  Backtrace:
      ▆
   1. ├─schtools::theme_lucas() at test-plot.R:11:1
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 49 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 77-94 [italic-genus] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggtext'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘uwot’
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown

Quitting from lines 82-125 [unnamed-chunk-8] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'uwot'
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'chromote', 'ggwordcloud', 'SemNetCleaner', 'tidytext', 'tidyxl'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recipes’

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', 'batchelor', 'Seurat', 'SeuratObject', 'harmony'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘PINSPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'ggtree', 'parallelDist', 'phangorn', 'Rcpp', 'reshape2',
  'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fgsea', 'reshape2', 'Rcpp', 'Rmisc', 'ggpubr', 'sccore', 'NMF',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'coda.base', 'simplifyEnrichment', 'WGCNA', 'conos', 'pagoda2', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Seurat', 'GSVA', 'pcaMethods', 'gProfileR', 'gprofiler2', 'ADAPTS',
  'reshape'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'SeuratObject'
Packages required but not available: 'alakazam', 'shazam', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘CIARA’
Note: skipping ‘SCOPRO_vignette.Rmd’ due to unavailable dependencies:
  'CIARA'
Packages required but not available: 'car', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

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

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: 'ks', 'cubature'

Packages which this enhances but not available for checking:
  'RcppEigen', 'RcppXPtrUtils'

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: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘crch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘scoringRules’

Package suggested but not available for checking: ‘ggdist’

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:
  'dynutils', 'dynwrap', 'lmds', 'princurve', 'ranger', 'reshape2'

Packages suggested but not available for checking:
  'anndata', 'reticulate', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'car', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Seurat', 'rdist', 'energy'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘scan’

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

Package suggested but not available for checking: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AUCell', 'clusterProfiler', 'enrichplot', 'ggdist', 'ggExtra',
  'ggrepel', 'infercnv', 'Nebulosa', 'plyr', 'qpdf', 'Seurat',
  'SeuratObject', 'sf', 'UCell'
Packages unavailable to check Rd xrefs: ‘infercnv’, ‘UCell’
Package required but not available: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘imager’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'splatter', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘scDHA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rtsne', 'TPEA', 'Rmisc', 'plyr', 'reshape2'

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

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

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'RSpectra', 'scTenifoldNet'

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

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

Package which this enhances but not available for checking: ‘glmGamPoi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘smotefamily’

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

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

Error: processing vignette 'SDaA_using_survey.Rnw' failed with diagnostics:
 chunk 2 (label = loadPkg) 
Error in library(survey) : there is no package called ‘survey’

--- failed re-building ‘SDaA_using_survey.Rnw’

SUMMARY: processing the following file failed:
  ‘SDaA_using_survey.Rnw’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sda.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:24: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shinythemes', 'shiny', 'shinyjs', 'shinyTree', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cffr', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'car', 'Rcpp', 'shiny', 'DT', 'shinyBS', 'VIM'

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: ‘raster’

Package suggested but not available for checking: ‘sf’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fda’

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: 'rnaturalearth', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geosphere', 'ggmap', 'sf', 'stars', 'ggspatial'

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

Package suggested but not available for checking: ‘reshape2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fmesher', 'lme4', 'TMB', 'RcppEigen'

Packages suggested but not available for checking:
  'DHARMa', 'effects', 'ggforce', 'glmmTMB', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dismo', 'maxnet', 'Rcpp', 'terra'

Packages suggested but not available for checking:
  'plotROC', 'rasterVis', 'reshape2'

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: 'plm', 'RSpectra', 'sf', 'spdep'

Package suggested but not available for checking: ‘splm’

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: ‘GB2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘PolynomF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geosphere', 'pander', 'sf', 'spdep', 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spelling', 'DT'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [25s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(sdtm.oak)
  > 
  > test_check("sdtm.oak")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 340 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-derive_blfl.R:39:3', 'test-derive_blfl.R:47:3',
    'test-derive_blfl.R:87:3', 'test-derive_blfl.R:96:3',
    'test-derive_blfl.R:123:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dataset_oak_vignette.R:33:3'): dataset_oak_vignette Test 2: A 'shiny.tag.list' is outputted when run inside pkgdown ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'DT'
  Backtrace:
       ▆
    1. ├─testthat::expect_s3_class(dataset_oak_vignette(dm), "shiny.tag.list") at test-dataset_oak_vignette.R:33:3
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─sdtm.oak:::dataset_oak_vignette(dm)
    5. │ └─htmltools::tagList(...)
    6. │   └─rlang::dots_list(...)
    7. └─base::loadNamespace(x)
    8.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9.     └─base (local) withOneRestart(expr, restarts[[1L]])
   10.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 340 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘oce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'shinyjs', 'shinyWidgets', 'plotly', 'DT',
  'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘crypto2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'seasonalview', 'spelling'
Packages required but not available: 'shinydashboard', 'shiny', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) seas.check.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:58: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘forecast’

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

Package suggested but not available for checking: ‘waterData’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘optimization’

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

Packages suggested but not available for checking: 'secrlinear', 'ipsecr'

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: 'secr', 'sf'

Package suggested but not available for checking: ‘secrdesign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'Rcpp', 'RcppNumerical', 'sf', 'terra', 'RcppEigen'

Packages suggested but not available for checking: 'gdistance', 'spsurvey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DDD', 'ape', 'geiger', 'Rcpp', 'treestats'

Packages suggested but not available for checking:
  'diversitree', 'phytools'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggmsa', 'msa'

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

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'demography', 'Rcpp', 'reshape2', 'LaF', 'openxlsx', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'DHARMa', 'factoextra', 'ggdag', 'ggdist', 'ggraph',
  'ggrepel', 'glmmTMB', 'lme4', 'merDeriv', 'qqplotr', 'RcppEigen',
  'rstanarm'
Packages required but not available: 'forecast', 'forecTheta', 'tsfeatures'

Packages suggested but not available for checking:
  'repmis', 'Mcomp', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FactoMineR’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'plyr', 'reshape2', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'leaflet', 'adehabitatLT', 'moveHMM', 'move', 'devtools', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'imputeTS', 'greybox', 'philentropy', 'Rfast', 'narray'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'

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: 'sf', 'units'

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

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

Packages suggested but not available for checking: 'tidycensus', 'tigris'

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

Package suggested but not available for checking: ‘polymapR’

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: 'arm', 'DescTools', 'ggpubr'

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: ‘factoextra’

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'Rfast', 'Cascade', 'varbvs'

Package suggested but not available for checking: ‘mixOmics’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'adaptMCMC', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'latticeExtra', 'ade4', 'FD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘Ecdat’
Packages suggested but not available for checking:
  'chromote', 'RSelenium', 'shiny', 'shinytest2', 'wdman'
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(selenider)
  > 
  > test_check("selenider")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/selenider.Rcheck/tests/testthat/setup-disable-crashpad.R"
  Caused by error in `loadNamespace()`:
  ! there is no package called 'chromote'
  Backtrace:
       ▆
    1. ├─testthat::test_check("selenider")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. ├─base::loadNamespace(x) at tests/testthat/setup-disable-crashpad.R:3:1
   15. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   16. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   17. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   18. │ └─base::stop(cond)
   19. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   20.   └─rlang::abort(...)
  Execution halted
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'shiny.semantic'
Running examples in ‘semantic.assets-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: uirender
> ### Title: Render semanticui htmlwidget
> ### Aliases: uirender
> 
> ### ** Examples
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Packages required but not available: 'shiny', 'shiny.semantic'

Package suggested but not available for checking: ‘shinydashboard’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SEMgraph', 'cito', 'NeuralNetTools', 'ranger', 'shapr', 'torch'

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

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

Package suggested but not available for checking: ‘piecewiseSEM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rsyntax’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSNNS', 'ks', 'StatMatch'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'energy', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘splines2’
Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Code.Rmd’ using rmarkdown

Quitting from lines 571-1013 [unnamed-chunk-8] (Code.Rmd)
Error: processing vignette 'Code.Rmd' failed with diagnostics:
there is no package called 'splines2'
--- failed re-building ‘Code.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘DiagrammeRsvg’

Package which this enhances but not available for checking: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

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

Packages suggested but not available for checking: 'Amelia', 'bmemLavaan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'leaflet', 'urlshorteneR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) append.dictionary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:89-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:113: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'plyr', 'qgraph', 'car', 'effects', 'philentropy'

Packages suggested but not available for checking:
  'shiny', 'shinyjs', 'shinyalert', 'shinyMatrix', 'shinyBS',
  'spreadr', 'animation', 'NetworkToolbox', 'SemNetCleaner'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qgraph', 'sem', 'plyr', 'rockchalk', 'OpenMx'

Package suggested but not available for checking: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘covsim’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Amelia', 'blavaan', 'mice'
checkRd: (-1) PAVranking.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:80-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
Running examples in ‘semTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: combinequark
> ### Title: Combine the results from the quark function
> ### Aliases: combinequark
> 
> ### ** Examples
> 
> 
> set.seed(123321)
> dat <- HolzingerSwineford1939[,7:15]
> misspat <- matrix(runif(nrow(dat) * 9) < 0.3, nrow(dat))
> dat[misspat] <- NA
> dat <- cbind(HolzingerSwineford1939[,1:3], dat)
> 
> quark.list <- quark(data = dat, id = c(1, 2))
Data Check Passed.
ID Check Passed.
Loading required namespace: mice
Failed with error:  ‘there is no package called ‘mice’’
The quark function requires the "mice" package to be installed.
> 
> final.data <- combinequark(quark = quark.list, percent = 80)
Error in if (pct[i] >= percent) { : argument is of length zero
Calls: combinequark
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘OpenMx’

Package suggested but not available for checking: ‘ctsemOMX’

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.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘emayili’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DescTools', 'shiny', 'shinydashboard', 'DT', 'plotly', 'cicerone',
  'reticulate'

Package suggested but not available for checking: ‘shinycssloaders’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sendmail_options.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:38-39: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘fixest’
Packages suggested but not available for checking:
  'ranger', 'glmnet', 'FSelectorRcpp', 'lme4'
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ape', 'phylolm', 'caper', 'phytools', 'geiger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'relaimpo', 'ggrepel', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'dtwclust', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ggExtra', 'IncDTW', 'ks', 'mc2d', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FactoMineR', 'factoextra', 'fields', 'plotly', 'shiny', 'reshape2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'ggmap'

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

Packages suggested but not available for checking:
  'tokenizers.bpe', 'word2vec'

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

Package suggested but not available for checking: ‘text2vec’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘TSdist’

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

Package suggested but not available for checking: ‘tm’

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

Packages suggested but not available for checking:
  'plotly', 'stm', 'topicmodels', 'seededlda', 'keyATM', 'servr',
  'sentometrics', 'spacyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'geoTS', 'eBsc', 'dtwclust'

Packages suggested but not available for checking: 'TSclust', 'bigmemory'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                               ^
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                                                          ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
Packages required but not available: 'plyr', 'phangorn', 'qvalue', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘matchingR’

Packages suggested but not available for checking: 'DESeq2', 'qvalue'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'FactoMineR', 'ade4', 'questionr'
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dHSIC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Amelia', 'plyr', 'ranger', 'mice'

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.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SKAT’
GNU make is a SystemRequirements.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘qs’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

Packages suggested but not available for checking:
  'openxlsx', 'vcfR', 'adegenet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Packages suggested but not available for checking:
  'dbscan', 'GA', 'keras', 'Rtsne', 'smacof', 'tensorflow', 'umap'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

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

Package suggested but not available for checking: ‘DT’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httpuv’

Package suggested but not available for checking: ‘later’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qgraph’
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
Running examples in ‘SEset-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: network_to_SEset
> ### Title: SE-set from precision matrix
> ### Aliases: network_to_SEset
> 
> ### ** Examples
> 
> # first estimate the precision matrix
> data(riskcor)
> omega <- (qgraph::EBICglasso(riskcor, n = 69, returnAllResults = TRUE))$optwi
Error in loadNamespace(x) : there is no package called ‘qgraph’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reticulate’
Package suggested but not available for checking: ‘forecast’
Packages required but not available: 'QCA', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘do’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'spam', 'RcppEigen'

Packages suggested but not available for checking: 'BPCells', 'sf'

Package which this enhances but not available for checking: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SeuratObject', 'ggrepel', 'leiden', 'miniUI', 'plotly', 'Rcpp',
  'RcppAnnoy', 'RcppHNSW', 'reticulate', 'RSpectra', 'Rtsne',
  'sctransform', 'shiny', 'uwot', 'RcppEigen'

Packages suggested but not available for checking:
  'ape', 'BPCells', 'MAST', 'DESeq2', 'Rfast2', 'monocle', 'metap',
  'mixtools', 'presto', 'harmony'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'cubature', 'fastGHQuad', 'mnorm', 'plm', 'trustOptim'

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

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

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'

Package suggested but not available for checking: ‘ggraph’

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: ‘sf’

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

Packages suggested but not available for checking: 'dbscan', 'sfnetworks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'geometries'

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

Package suggested but not available for checking: ‘ggspatial’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lwgeom', 'sf', 'sfheaders', 'units'

Packages suggested but not available for checking: 'dbscan', 's2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Error(s) in re-building vignettes:
  ...
--- re-building ‘v1_intro.Rmd’ using rmarkdown
--- finished re-building ‘v1_intro.Rmd’

--- re-building ‘v3_analyzing_landing.Rmd’ using rmarkdown

Quitting from lines 30-37 [unnamed-chunk-2] (v3_analyzing_landing.Rmd)
Error: processing vignette 'v3_analyzing_landing.Rmd' failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘v3_analyzing_landing.Rmd’

SUMMARY: processing the following file failed:
  ‘v3_analyzing_landing.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 's2', 'units', 'Rcpp'

Packages suggested but not available for checking:
  'lwgeom', 'mapview', 'odbc', 'pool', 'raster', 'stars', 'terra',
  'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘DescTools’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

Packages suggested but not available for checking:
  'stars', 'sftrack', 'cubble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘wordspace’

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

Packages suggested but not available for checking:
  'adehabitatLT', 'geosphere', 'lwgeom'

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.
Package required but not available: ‘sf’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GBJ’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggforce’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘conquer’

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

Packages suggested but not available for checking: 'bigmemory', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plotly', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ModelMetrics’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘sGMRFmix.Rmd’ using rmarkdown

Quitting from lines 13-24 [unnamed-chunk-1] (sGMRFmix.Rmd)
Error: processing vignette 'sGMRFmix.Rmd' failed with diagnostics:
there is no package called 'ModelMetrics'
--- failed re-building ‘sGMRFmix.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘SGP’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGPdata.Rmd’ using rmarkdown

Quitting from lines 2-11 (SGPdata.Rmd)
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
there is no package called 'toOrdinal'
--- failed re-building ‘SGPdata.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘mixOmics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘collapse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'caret', 'faux', 'SLOPE', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'glmnet', 'grpSLOPE'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'terra', 'clhs', 'BalancedSampling'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                   ^
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                                                                                                                                        ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RSelenium’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘coneproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mice’
checkRd: (-1) powerShape.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:32-33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Running examples in ‘shapeNA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: barplot.shapeNA
> ### Title: Barplot Showcasing Missingness Proportion of the Original Data
> ### Aliases: barplot.shapeNA
> 
> ### ** Examples
> 
>     S <- toeplitz(seq(1, 0.1, length.out = 3))
>     x <- mvtnorm::rmvt(100, S, df = 5)
>     y <- mice::ampute(x, mech='MCAR')$amp
Error in loadNamespace(x) : there is no package called ‘mice’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'terra', 'landscapemetrics', 'raster'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cellWise', 'robustHD'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ShapleyOutlier_examples.Rmd’ using rmarkdown

Quitting from lines 27-32 [unnamed-chunk-2] (ShapleyOutlier_examples.Rmd)
Error: processing vignette 'ShapleyOutlier_examples.Rmd' failed with diagnostics:
there is no package called 'robustHD'
--- failed re-building ‘ShapleyOutlier_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘waffle’

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

Package suggested but not available for checking: ‘qpdf’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggfittext', 'gggenes', 'ggrepel'

Package which this enhances but not available for checking: ‘fastshap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘interp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'np'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fake', 'glmnet'

Packages suggested but not available for checking:
  'dbscan', 'mixOmics', 'OpenMx', 'randomcoloR', 'rCOSA', 'sgPLS'

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

Packages suggested but not available for checking:
  'spdep', 'terra', 'raster', 'exactextractr', 'hydromad',
  'latticeExtra', 'daymetr', 'elevatr', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dcmle', 'dclone'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Ryacas', 'NMF'

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

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:
  'flexsurv', 'ggExtra', 'shiny', 'shinyMatrix', 'survminer'

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rtop', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qpdf', 'dpseg', 'tableHTML', 'devtools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘ggExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘pander’
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown

Quitting from lines 14-20 [loadKnitr] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'AER', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [32s/42s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ShiftShareSE)
  > 
  > test_check("ShiftShareSE")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 50 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_adh.R:28:5'): Point estimates match Table 3 ────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'AER'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_adh.R:28:5
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_se.R:53:5'): Homoscedastic and EHW standard errors on ADH data ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'AER'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_se.R:53:5
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 50 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DT', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'colourpicker', 'shinydisconnect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

Packages suggested but not available for checking:
  'shinydashboard', 'shinytest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shinytest2’

Package suggested but not available for checking: ‘spelling’

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

Package suggested but not available for checking: ‘shiny.router’

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

Packages suggested but not available for checking:
  'cmdstanr', 'shinystan', 'rstanarm', 'lme4', 'shinytest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘shinydisconnect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggiraph', 'shiny', 'shinyWidgets', 'shinyGizmo'

Package suggested but not available for checking: ‘shinyQueryBuilder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'DT', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinydisconnect', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘shinycssloaders’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'fresh', 'waiter'

Packages suggested but not available for checking:
  'shinyAce', 'shinyWidgets', 'shinyEffects', 'shinyjqui'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'DT', 'billboarder', 'scrypt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'shinytest2', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘colourpicker’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinydashboard', 'shinydashboardPlus', 'bs4Dash'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'chromote', 'shinytest2', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Packages required but not available:
  'shiny', 'DT', 'qvalue', 'Rfast', 'shinyhelper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

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

Packages suggested but not available for checking:
  'chromote', 'DT', 'imola', 'leaflet', 'plotly', 'shiny.i18n',
  'shiny.router', 'shinyjs', 'shinytest2', 'sortable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shinyWidgets’

Package which this enhances but not available for checking: ‘shiny’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'rhino', 'shinyAce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinycssloaders', 'mirt'

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

Packages suggested but not available for checking:
  'difNLR', 'DT', 'latticeExtra', 'plotly', 'shiny', 'shinyBS',
  'shinydashboard', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinyAce', 'shinydisconnect'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

Package suggested but not available for checking: ‘websocket’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'fastLink', 'golem', 'shiny', 'shinydashboard',
  'shinydashboardPlus', 'shinyWidgets'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'httpuv', 'spelling'
Packages required but not available: 'httpuv', 'websocket'

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'DT', 'billboarder', 'scrypt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinyjqui', 'shinythemes', 'uchardet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘shinyAce’

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

Packages suggested but not available for checking: 'learnr', 'shinytest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'argonDash', 'shinyjs', 'shinyWidgets', 'plotly', 'DT',
  'shinycssloaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinyWidgets', 'apexcharter', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'plotly', 'shiny', 'shinydashboard', 'tune'

Packages suggested but not available for checking:
  'finetune', 'shinytest', 'spelling'

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

Package suggested but not available for checking: ‘chipPCR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinythemes', 'uchardet', 'shinyjqui'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'shinyWidgets', 'Ternary'

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

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

Package suggested but not available for checking: ‘spelling’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'DT', 'shinythemes', 'Epi'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'shiny', 'urltools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinyWidgets', 'miniUI', 'shinyjs',
  'shinyFiles', 'shinyalert', 'colourpicker', 'plotly', 'reshape2'

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

Package suggested but not available for checking: ‘sortable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'chromote', 'leaflet', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'recipes', 'shiny', 'miniUI', 'shinyWidgets', 'shinyglide',
  'sortable', 'DT', 'esquisse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

Packages suggested but not available for checking:
  'DT', 'devtools', 'emayili', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sbm', 'colourpicker', 'DT', 'flextable', 'fresh', 'golem', 'shiny',
  'shinyalert', 'shinydashboard'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘timevis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'jsTreeR', 'shiny'
Running examples in ‘shinySelect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HTMLchoices
> ### Title: Choices with HTML
> ### Aliases: HTMLchoices
> 
> ### ** Examples
> 
> library(shinySelect)
> library(fontawesome)
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'chromote', 'DT', 'leaflet', 'plotly', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'bayesplot', 'colourpicker', 'DT', 'reshape2', 'rstan',
  'shinyjs', 'shinythemes'

Packages suggested but not available for checking: 'cmdstanr', 'rstanarm'

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

Package suggested but not available for checking: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

Packages suggested but not available for checking:
  'DT', 'plotly', 'plumber', 'semantic.dashboard', 'shiny.semantic',
  'shinyjs', 'timevis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'forecast', 'ggpmisc', 'ggtree', 'golem', 'shiny',
  'shinydashboard', 'shinyjs', 'shinyWidgets', 'treeio'

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

Packages suggested but not available for checking:
  'plotly', 'shinyWidgets', 'shinytest', 'shinyvalidate', 'spelling'

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

Package suggested but not available for checking: ‘flexdashboard’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'DT', 'shinydashboard', 'shinydashboardPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'shinythemes', 'shinydashboard', 'shinyWidgets',
  'shinyjs', 'reshape2', 'shinytest2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > shinytest2::test_app()
  Error in loadNamespace(x) : there is no package called 'shinytest2'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'apcluster', 'ape', 'dbscan', 'ips', 'phangorn', 'StatMatch'
checkRd: (-1) MrBayes.Rd:24: Lost braces
    24 | \item{contype}{A character string; the type of consensus tree calculated from the posterior distribution of trees}{either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)}
       |                                                                                                                   ^
Packages required but not available: 'ggrepel', 'ggspatial', 'sf', 'terra'

Packages suggested but not available for checking:
  'elevatr', 'rnaturalearth'

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

Package suggested but not available for checking: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘TAM’

Packages suggested but not available for checking: 'sirt', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘LambertW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'energy', 'shiny', 'interp', 'bs4Dash'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'stochvol', 'RcppArmadillo', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'shrinkTVP', 'stochvol', '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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) shutterplot.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'difNLR', 'DT', 'lme4', 'mirt', 'mirtCAT', 'plotly', 'shiny',
  'ShinyItemAnalysis', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘hdrcde’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘multicool’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pcalg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggpubr', 'plyr', 'np', 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) drr.Rd:36: Lost braces; missing escapes or markup?
    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
Specified C++11: please drop specification unless essential
Packages required but not available: 'plyr', 'survey'

Packages suggested but not available for checking:
  'car', 'GGally', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

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

Packages suggested but not available for checking:
  'ggcorrplot', 'ggfittext', 'ggrepel', 'reticulate', 'synchronicity'

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

Packages suggested but not available for checking:
  'Seurat', 'ggforce', 'ggrepel', 'chromVAR', 'TFBSTools',
  'motifmatchr', 'shiny', 'miniUI'

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

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

Packages suggested but not available for checking: 'DT', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘survminer’

Package suggested but not available for checking: ‘Rmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

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

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: ‘ggraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘signs.Rmd’ using rmarkdown

Quitting from lines 18-23 [setup] (signs.Rmd)
Error: processing vignette 'signs.Rmd' failed with diagnostics:
there is no package called 'ggrepel'
--- failed re-building ‘signs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available:
  'ape', 'phylobase', 'phyext2', 'phyloseq'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: p_sie
> ### Title: Get data for p-SIE curve
> ### Aliases: p_sie
> 
> ### ** Examples
> 
> library(ggplot2)
> library(tidyfst)
Error in library(tidyfst) : there is no package called ‘tidyfst’
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(siie)
  > 
  > test_check("siie")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-p_sie.R:4:3'): p_sie ───────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(tidyfst)`: there is no package called 'tidyfst'
  Backtrace:
      ▆
   1. └─base::library(tidyfst) at test-p_sie.R:4:3
  ── Error ('test-prp.R:4:3'): prp ───────────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(tidyfst)`: there is no package called 'tidyfst'
  Backtrace:
      ▆
   1. └─base::library(tidyfst) at test-prp.R:4:3
  ── Error ('test-siie.R:5:3'): siie ─────────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(tidyfst)`: there is no package called 'tidyfst'
  Backtrace:
      ▆
   1. └─base::library(tidyfst) at test-siie.R:5:3
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 33-37 [unnamed-chunk-3] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'tidyfst'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'sf', 'lme4', 'raster', 'ggforce', 'fasterize', 'reshape2', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'Ckmeans.1d.dp'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘decido’

Package suggested but not available for checking: ‘trip’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Thresher’

Packages suggested but not available for checking: 'Mercator', 'Umpire'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spam’

Package suggested but not available for checking: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'spelling', 'ggExtra'
Packages suggested but not available for checking: 'MatchIt', 'openxlsx'
Error(s) in re-building vignettes:
  ...
--- re-building ‘sim.BA.Rmd’ using rmarkdown

Quitting from lines 79-98 [unnamed-chunk-4] (sim.BA.Rmd)
Error: processing vignette 'sim.BA.Rmd' failed with diagnostics:
The package "MatchIt" is required.
--- failed re-building ‘sim.BA.Rmd’

SUMMARY: processing the following file failed:
  ‘sim.BA.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'RcppXPtrUtils', 'RcppArmadillo'

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'mirt', 'mirtCAT', 'shiny', 'shinycssloaders'

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 checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘multgee’
Running examples in ‘SimCorMultRes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rmult.acl
> ### Title: Simulating Correlated Ordinal Responses Conditional on a
> ###   Marginal Adjacent-Category Logit Model Specification
> ### Aliases: rmult.acl
> 
> ### ** Examples
> 
> ## See Example 3.4 in the Vignette.
> beta_intercepts <- c(3, 1, 2)
> beta_coefficients <- c(1, 1)
> sample_size <- 500
> cluster_size <- 3
> set.seed(321)
> x1 <- rep(rnorm(sample_size), each = cluster_size)
> x2 <- rnorm(sample_size * cluster_size)
> xdata <- data.frame(x1, x2)
> identity_matrix <- diag(4)
> equicorrelation_matrix <- toeplitz(c(1, rep(0.95, cluster_size - 1)))
> latent_correlation_matrix <- kronecker(equicorrelation_matrix,
+   identity_matrix)
> simulated_ordinal_dataset <- rmult.acl(clsize = cluster_size,
+   intercepts = beta_intercepts, betas = beta_coefficients,
+   xformula = ~ x1 + x2, xdata = xdata,
+   cor.matrix = latent_correlation_matrix)
> suppressPackageStartupMessages(library("multgee"))
Error in library("multgee") : there is no package called ‘multgee’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SimCorMultRes.Rmd’ using rmarkdown
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.


Quitting from lines 72-107 [unnamed-chunk-2] (SimCorMultRes.Rmd)
Error: processing vignette 'SimCorMultRes.Rmd' failed with diagnostics:
there is no package called 'multgee'
--- failed re-building ‘SimCorMultRes.Rmd’

--- re-building ‘r_journal_paper.pdf.asis’ using asis
--- finished re-building ‘r_journal_paper.pdf.asis’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

Package suggested but not available for checking: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GGally', 'ggcorrplot', 'nhanesA', 'reshape2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Demo.Rmd’ using rmarkdown

Quitting from lines 20-27 [unnamed-chunk-1] (Demo.Rmd)
Error: processing vignette 'Demo.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘Demo.Rmd’

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

Quitting from lines 24-31 [unnamed-chunk-1] (NORTA_demo.Rmd)
Error: processing vignette 'NORTA_demo.Rmd' failed with diagnostics:
there is no package called 'nhanesA'
--- failed re-building ‘NORTA_demo.Rmd’

--- re-building ‘Technical_documentation.Rmd’ using rmarkdown
--- finished re-building ‘Technical_documentation.Rmd’

SUMMARY: processing the following files failed:
  ‘Demo.Rmd’ ‘NORTA_demo.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'shiny', 'extraDistr'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘minqa’

Package suggested but not available for checking: ‘FME’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘magick’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'bigmemory', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggpmisc', 'ggpubr', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'popkin', 'bnpsd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppSimdJson’

Package suggested but not available for checking: ‘spelling’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'shiny'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Packages required but not available: 'fastGHQuad', 'ICSKAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'prodlim', 'rpact'
Error(s) in re-building vignettes:
  ...
--- re-building ‘correlation.Rmd’ using rmarkdown
--- finished re-building ‘correlation.Rmd’

--- re-building ‘pwc_survival.Rmd’ using rmarkdown
--- finished re-building ‘pwc_survival.Rmd’

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

Quitting from lines 27-32 [unnamed-chunk-1] (quickstart.Rmd)
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
there is no package called 'prodlim'
--- failed re-building ‘quickstart.Rmd’

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

Quitting from lines 32-37 [unnamed-chunk-1] (trialplanning.Rmd)
Error: processing vignette 'trialplanning.Rmd' failed with diagnostics:
there is no package called 'prodlim'
--- failed re-building ‘trialplanning.Rmd’

SUMMARY: processing the following files failed:
  ‘quickstart.Rmd’ ‘trialplanning.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'rvinecopulib', 'bde', 'ks', 'np', 'extraDistr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
checkRd: (-1) internal.statistics.one.lm.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) internal.statistics.one.lm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_simitation.Rmd’ using knitr

Quitting from lines 38-39 [unnamed-chunk-2] (Introduction_to_simitation.Rmd)
Error: processing vignette 'Introduction_to_simitation.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘Introduction_to_simitation.Rmd’

--- re-building ‘Introduction_to_simitation_2.Rmd’ using knitr
--- finished re-building ‘Introduction_to_simitation_2.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'arm', 'plyr'
Running examples in ‘simITS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aggregate_simulation_results
> ### Title: Test a passed test statistic on the simulated data
> ### Aliases: aggregate_simulation_results
> 
> ### ** Examples
> 
> predictions = process_outcome_model( "pbail", mecklenberg,
+                                     t0=0, R = 5,
+                                     summarize = FALSE, smooth=FALSE )
Error in loadNamespace(x) : there is no package called ‘arm’
Calls: process_outcome_model ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_ITS_example.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/simITS.Rcheck/vign_test/simITS/vignettes/simple_ITS_example_files/figure-html/unnamed-chunk-1-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5401 bytes
Input file size = 6256 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5131
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5131

Output IDAT size = 5131 bytes (270 bytes decrease)
Output file size = 5209 bytes (1047 bytes = 16.74% decrease)


Quitting from lines 64-69 [unnamed-chunk-4] (simple_ITS_example.Rmd)
Error: processing vignette 'simple_ITS_example.Rmd' failed with diagnostics:
there is no package called 'arm'
--- failed re-building ‘simple_ITS_example.Rmd’

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

Error: Vignette re-building failed.
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:
  'bigmemory', 'gganimate', 'ks', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'Sie2nts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘simmer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘simmer’

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

Package suggested but not available for checking: ‘simmer.plot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Packages required but not available:
  'compositions', 'reshape2', 'bayesplot', 'Rcpp', 'GGally',
  'RcppArmadillo', 'RcppDist'

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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'miniPCH', 'car'

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

Packages suggested but not available for checking: 'nngeo', 'tmap'

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 suggested but not available for checking: ‘precrec’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) coxsimSpline.Rd:93: Lost braces; missing escapes or markup?
    93 | {FD(h[i](t)) = (exp(g(x[j]) - g(x[l])) - 1) * 100}
       | ^
checkRd: (-1) simPH.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:20-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:25-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:34-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:50-53: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
Packages suggested but not available for checking: 'devtools', 'spelling'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘verification’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sanic’

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

Package suggested but not available for checking: ‘pbkrtest’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Error(s) in re-building vignettes:
  ...
--- re-building ‘simrec-vignette.Rmd’ using rmarkdown

Quitting from lines 155-198 [Examplesimrec] (simrec-vignette.Rmd)
Error: processing vignette 'simrec-vignette.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘simrec-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘simrec-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'ontologySimilarity'

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

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

Packages suggested but not available for checking:
  'shinyBS', 'shinythemes', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Packages suggested but not available for checking:
  'adehabitatLT', 'moveHMM', 'sf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'Amelia', 'OpenMx'
checkRd: (-1) SimDataDist-class.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SimDataDist-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createData.Rd:7: Lost braces
     7 |         This function can be used to create data from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function is used internally to create data, and is available publicly for accessibility and debugging.
       |                                                                                                                         ^
checkRd: (-1) exportData.Rd:7: Lost braces
     7 |         This function can be used to export data created from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function can export data to be analyzed with either Mplus or LISREL.
       |                                                                                                                                 ^
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvnfast', 'Rcpp', 'fastglm', 'pbv'

Packages suggested but not available for checking:
  'gtsummary', 'survminer', 'katex'

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

Packages suggested but not available for checking:
  'fields', 'flexdashboard', 'shiny', 'lme4', 'INLA', 'INLAspacetime'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'flexsurv', 'rstpm2'
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
Error(s) in re-building vignettes:
  ...
--- re-building ‘simsurv_technical.Rmd’ using rmarkdown
--- finished re-building ‘simsurv_technical.Rmd’

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

Quitting from lines 15-23 [setup] (simsurv_usage.Rmd)
Error: processing vignette 'simsurv_usage.Rmd' failed with diagnostics:
there is no package called 'flexsurv'
--- failed re-building ‘simsurv_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'plyr'

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

Packages suggested but not available for checking:
  'gsDesign', 'gsDesign2', 'gt'

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: ‘ks’

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

Packages suggested but not available for checking:
  'magick', 'contoureR', 'raster', 'openair'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
checkRd: (-1) add_bold.Rd:15: Lost braces; missing escapes or markup?
    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'shiny', 'miniUI'
Packages suggested but not available for checking: 'lme4', 'lmerTest'
Error(s) in re-building vignettes:
  ...
--- re-building ‘singcar_vignette.Rmd’ using rmarkdown

Quitting from lines 78-84 [setup] (singcar_vignette.Rmd)
Error: processing vignette 'singcar_vignette.Rmd' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘singcar_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'spelling', 'shiny', 'purrrlyr', 'rclipboard'
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'SeuratObject', 'wrswoR', 'sparseMatrixStats'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinycssloaders', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'COVIDIBGE', 'PNADcIBGE', 'PNDSIBGE', 'PNSIBGE'

Packages suggested but not available for checking:
  'convey', 'srvyr', 'survey'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'HTSSIP', 'phyloseq', 'plyr', 'ggpubr', 'DESeq2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘raster’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘systemfit’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'CDM', 'Rcpp', 'TAM', 'pbv', 'RcppArmadillo'

Packages suggested but not available for checking:
  'miceadds', 'minqa', 'mirt', 'pbv', 'survey'

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

Package suggested but not available for checking: ‘ranger’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RSpectra', 'glmnet', 'Boruta', 'mixOmics', 'ranger', 'adjclust',
  'aricode', 'reshape2'

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: 'openxlsx', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sitar-package.Rd:27: Lost braces; missing escapes or markup?
    27 | individual curves, adjusted for {abcd} to lie on top of (i.e. be
       |                                 ^
checkRd: (-1) sitar.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{\link{nlme}}) (default {nlmeControl(returnObject = TRUE)}).}
       |                              ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MatchIt', 'reshape2'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gdalUtilities', 'Rcpp', 'rstac', 'sf', 'terra', 'torch', 'units',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'caret', 'dtwclust', 'exactextractr', 'gdalcubes', 'geojsonsf',
  'kohonen', 'leafem', 'leaflet', 'luz', 'openxlsx',
  'randomForestExplainer', 'RcppArmadillo', 'spdep', 'stars',
  'supercells', 'tmap'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘mice’
Packages suggested but not available for checking:
  'brms', 'car', 'effects', 'ggrepel', 'glmmTMB', 'lme4', 'rstanarm',
  'survey', 'TMB'
Packages required but not available: 'reticulate', 'ggtern', 'qgam'

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'car', 'lme4', 'survey'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘lme4’
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sjtable2df)
  > 
  > test_check("sjtable2df")
  [ FAIL 1 | WARN 4 | SKIP 4 | PASS 16 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-mtab2df.R:48:5', 'test-xtab2df.R:36:5',
    'test-xtab2df.R:206:5', 'test-xtab2df.R:253:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-mtab2df.R:117:5'): correct functioning of mtab2df: glmer ───────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-mtab2df.R:117:5
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 4 | SKIP 4 | PASS 16 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sjtable2df_overview.Rmd’ using rmarkdown

Quitting from lines 244-265 [unnamed-chunk-19] (sjtable2df_overview.Rmd)
Error: processing vignette 'sjtable2df_overview.Rmd' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘sjtable2df_overview.Rmd’

SUMMARY: processing the following file failed:
  ‘sjtable2df_overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘corrr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bazar', 'Rfast', 'caret', 'osqp', 'ROI.plugin.qpoases'

Packages suggested but not available for checking:
  'devtools', 'car', 'cubature'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘imager’

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

Package suggested but not available for checking: ‘ivreg’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggrepel', 'MomTrunc', 'relliptical', 'TruncatedNormal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggpubr', 'reshape2', 'FastGaSP', 'Rcpp', 'RcppEigen'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘kmndirs’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'Rcpp', 'car', 'lmerTest', 'RcppEigen'

Packages suggested but not available for checking:
  'mbest', 'rintrojs', 'shinythemes', 'shiny', 'shinyjs', 'gt',
  'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rnaturalearth', 'terra'
Packages required but not available: 'swephR', 'oce', 'MESS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘texPreview’
Package which this enhances but not available for checking: ‘spam’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'forecast', 'imputeTS', 'MTS', 'TSclust', 'tsoutliers'

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: 'reda', 'reReg'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'DT', 'shiny', 'shinycssloaders', 'shinyWidgets'

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

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

Package suggested but not available for checking: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reticulate', 'ape', 'shinyWidgets', 'shiny'

Packages suggested but not available for checking:
  'sf', 'stars', 'rnaturalearth', 'gganimate', 'units', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'CCA', 'car'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'captioner', 'rcrossref'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'pdftools', 'leaflet'
checkRd: (-1) nba_team_logo.Rd:22: Lost braces; missing escapes or markup?
    22 | https://i.cdn.turner.com/nba/nba/.element/img/4.0/global/logos/512x512/bg.white/svg/{team_short_name}.svg
       |                                                                                     ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
--- finished re-building ‘basics.Rmd’

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

Quitting from lines 82-91 [unnamed-chunk-9] (doms.Rmd)
Error: processing vignette 'doms.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building ‘doms.Rmd’

--- re-building ‘iframes.Rmd’ using rmarkdown
--- finished re-building ‘iframes.Rmd’

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

Quitting from lines 11-18 [unnamed-chunk-1] (pdfs.Rmd)
Error: processing vignette 'pdfs.Rmd' failed with diagnostics:
there is no package called 'pdftools'
--- failed re-building ‘pdfs.Rmd’

--- re-building ‘plots.Rmd’ using rmarkdown
--- finished re-building ‘plots.Rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
--- finished re-building ‘shiny.Rmd’

--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
--- finished re-building ‘tests_and_coverage.Rmd’

SUMMARY: processing the following files failed:
  ‘doms.Rmd’ ‘pdfs.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nonlinearTseries’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'jmcm'
checkRd: (-1) fit_slim.Rd:24: Lost braces; missing escapes or markup?
    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘slim.Rmd’ using rmarkdown

Quitting from lines 168-175 [unnamed-chunk-12] (slim.Rmd)
Error: processing vignette 'slim.Rmd' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘slim.Rmd’

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

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

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.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'caret', 'glmnet', 'spelling'

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.
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘ibd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'weights', 'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'smacof', 'minqa', 'ProjectionBasedClustering', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘smerc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sdcHierarchies’
Packages required but not available: 'flextable', 'ggtext', 'reticulate'

Package suggested but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'matlib', 'pryr'

Package suggested but not available for checking: ‘faraway’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'qpdf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
Packages required but not available: 'leaflet', 'sf'

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

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rfast', 'RSpectra', 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pROC’

Packages suggested but not available for checking: 'reshape2', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) trlong.Rd:17: Lost braces
    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
Packages required but not available: 'GSVA', 'samr', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'gt', 'mice', 'naniar', 'pROC', 'tableone'

Packages suggested but not available for checking: 'gtsummary', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'paws.compute', 'paws.developer.tools', 'paws.machine.learning',
  'paws.management', 'paws.storage', 'paws.security.identity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tableone’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'SpatialEpi', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'weights'

Packages suggested but not available for checking:
  'mlmRev', 'Kernelheaping'

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

Package suggested but not available for checking: ‘hdrcde’

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

Package suggested but not available for checking: ‘spelling’

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.
Package required but not available: ‘sf’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘splines2’

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘demography’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘prodlim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'SpatialVx', 'fields'
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'greybox', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘legion’

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: 'sf', 'terra', 'units'

Package suggested but not available for checking: ‘lwgeom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘logcondens’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘Rfast’

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: 'fields', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dbscan’

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.
Package suggested but not available for checking: ‘revdbayes’
Running examples in ‘smovie-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ett
> ### Title: Extremal Types Theorem (ETT)
> ### Aliases: ett
> 
> ### ** Examples
> 
> # Exponential data: xi = 0
> ett()
Error: the revdbayes package is needed. Please install it.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'flextable', 'plotROC', 'icenReg'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DescTools', 'shiny', 'shinydashboard', 'sortable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggraph', 'graphlayouts', 'miniUI', 'shiny', 'colourpicker', 'DT'

Package suggested but not available for checking: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘purrrlyr’
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("tibble")
  > library("snakecase")
  > 
  > 
  > test_check("snakecase")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 292 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-to_any_case.R:674:3'): expand.grid ─────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'purrrlyr'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-to_any_case.R:674:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 292 ]
  Error: Test failures
  Execution halted
checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'terra', 'raster', 'sf', 'units'
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
checkRd: (-1) sk_GLS.Rd:40: Lost braces; missing escapes or markup?
    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
checkRd: (-1) sk_LL.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
checkRd: (-1) sk_var.Rd:41: Lost braces; missing escapes or markup?
    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
checkRd: (-1) sk_var.Rd:33: Lost braces; missing escapes or markup?
    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘snapKrig_introduction.Rmd’ using rmarkdown

Quitting from lines 19-29 [unnamed-chunk-1] (snapKrig_introduction.Rmd)
Error: processing vignette 'snapKrig_introduction.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘snapKrig_introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'keras', 'tensorflow', 'dbscan', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘prodlim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinydashboard', 'leaflet', 'plotly', 'DT'

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: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

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

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

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: 'GWASTools', 'ggrepel', 'reshape2'

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: 'ggrepel', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape2’
checkRd: (-1) maize.line.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) raw.data.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{call.rate}{\code{numeric}. Threshold for removing marker by missing genotype rate. SNP with \code{call rate} below threshold are removed from dataset. Must be between {0, 1}}
       |                                                                                                                                                                              ^
checkRd: (-1) raw.data.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{maf}{Threshold for removing SNP by minor allele frequency. Must be between {0, 1}}
       |                                                                                  ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘snpReady-vignette.Rmd’ using rmarkdown

Quitting from lines 43-49 [unnamed-chunk-2] (snpReady-vignette.Rmd)
Error: processing vignette 'snpReady-vignette.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘snpReady-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘snpReady-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'gaston', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.selm.Rd:101: Lost braces
   101 | data. Default value for code{which} is \code{2:4} if \code{p>1}, otherwise
       |                             ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘astrochron’
Skipping checking math rendering: package 'V8' unavailable
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
Package required but not available: ‘lhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'np', 'minqa'

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:
  'shiny', 'FactoMineR', 'ggrepel', 'reshape2', 'flextable'

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: ‘oai’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

Packages suggested but not available for checking:
  'geosphere', 'sf', 'tigris', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                          ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                        ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                                     ^
checkRd: (-1) s_soda_pred.Rd:8: Lost braces; missing escapes or markup?
     8 | S-SODA assumes within each slice the X vector follow multivariate normal distribution. This function predicts the response y by reverting the P(X | slice(y)) to P(slice(y) | X), and estimates the E(y|X) as sum_{h} E(y | slice(y)=h, X) P (slice(y)=h | X)
       |                                                                                                                                                                                                                   ^
Package required but not available: ‘crul’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'shinyjs', 'ggExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'raster', 'sf', 'terra'

Packages suggested but not available for checking:
  'arm', 'Cubist', 'ranger', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'odbc', 'sf', 'terra', 'raster'
Error loading dataset 'gopheridge':
   Error in .requirePackage(package) : unable to find required package 'sp'
  
  Error loading dataset 'loafercreek':
   Error in .requirePackage(package) : unable to find required package 'sp'
  
  Error loading dataset 'mineralKing':
   Error in .requirePackage(package) : unable to find required package 'sp'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinydashboard', 'fields'

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 suggested but not available for checking: ‘FME’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ape’
Package required but not available: ‘AICcmodavg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘raster’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘latticeExtra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘latticeExtra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

Package suggested but not available for checking: ‘uwot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'shinyjs'
checkRd: (-1) solve_pH_from_AT.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:93: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'recipes', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Packages required but not available:
  'shiny', 'ggwordcloud', 'metR', 'interp'

Packages suggested but not available for checking:
  'shinycssloaders', 'shinyBS', 'shinyjs', 'shinyjqui'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'kohonen', 'shiny', 'plyr', 'openair', 'colourpicker',
  'shinycssloaders', 'shinycustomloader'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bio3d', 'kohonen'

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: 'plyr', 'RSpectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘IntervalSurgeon’

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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'kohonen', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geosphere’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'devtools', 'reticulate', 'soundecology', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘SpATS’
Running examples in ‘SOP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rae
> ### Title: Defining random effects in SOP formula
> ### Aliases: rae
> ### Keywords: models smooth regression
> 
> ### ** Examples
> 
> library(SOP)
> require(SpATS)
Loading required package: SpATS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘SpATS’
> ## An example of use of SOP package for the analysis of field trials experiments.
> ## Taken from the SpATS package.
> data(wheatdata)
Warning in data(wheatdata) : data set ‘wheatdata’ not found
> 
> # Create factor variable for row and columns
> wheatdata$R <- as.factor(wheatdata$row)
Error: object 'wheatdata' not found
Execution halted
Skipping checking math rendering: package 'V8' unavailable
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: 'learnr', 'shiny'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) spe.Rd:101: Lost braces
   101 | code{spe} command; (4) \code{alpha} stores significance level as in
       |     ^
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RefManageR’

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyBS', 'shinyFiles', 'shiny', 'keras', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘oce’

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

Package which this enhances but not available for checking: ‘RecordLinkage’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'shinyBS', 'shiny', 'shinyjs', 'nonlinearTseries'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Seurat’

Packages suggested but not available for checking: 'rstan', 'DropletUtils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpubr', 'golem', 'shiny', 'shinydashboard'

Package suggested but not available for checking: ‘gridlayout’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'NAM', 'lme4', 'reshape2', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DT', 'urltools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'sftime', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'adehabitatLT', 'cshapes', 'gstat', 'plm', 'raster', 'sf', 'sftime'
Error(s) in re-building vignettes:
  ...
--- re-building ‘jss816.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Error: processing vignette 'jss816.Rnw' failed with diagnostics:
 chunk 23 
Error in eval(expr, .GlobalEnv) : object 'nc' not found

--- failed re-building 'jss816.Rnw'

--- re-building ‘sto.Rnw’ using Sweave

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

--- finished re-building ‘sto.Rnw’

--- re-building ‘stpg.Rnw’ using Sweave
Warning: undefined slot classes in definition of "ST_PG": con(class "PostgreSQLConnection")
--- finished re-building ‘stpg.Rnw’

--- re-building ‘stsubs.Rnw’ using Sweave
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

--- finished re-building ‘stsubs.Rnw’

SUMMARY: processing the following file failed:
  ‘jss816.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'quickPlot', 'qs', 'terra'

Packages suggested but not available for checking:
  'NLMR', 'raster', 'SpaDES.tools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'quickPlot', 'SpaDES.core', 'SpaDES.tools'

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

Packages suggested but not available for checking:
  'animation', 'dqrng', 'NLMR', 'quickPlot', 'raster', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'earlywarnings', 'np'
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spam’
Running examples in ‘spam64-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spam64-package
> ### Title: 64-bit extension for the SPArse Matrix Package spam
> ### Aliases: spam64-package spam64 SPAM64 Spam64
> ### Keywords: documentation package
> 
> ### ** Examples
> 
> library("spam")
Error in library("spam") : there is no package called ‘spam’
Execution halted
Packages required but not available:
  'Rcpp', 'minqa', 'geometry', 'RcppEigen'

Packages suggested but not available for checking:
  'Infusion', 'IsoriX', 'blackbox', 'RSpectra', 'lme4'

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

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

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'car', 'DT', 'shinyBS', 'shinythemes', 'spdep', 'ape',
  'spatialreg', 'shinycssloaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'ptw', 'mmand', 'RNifti', 'RNiftyReg', 'fields'

Packages suggested but not available for checking: 'shiny', 'miniUI', 'car'

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
Package required but not available: ‘sparklyr.nested’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘listviewer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'reshape2', 'shiny'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

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

Packages suggested but not available for checking:
  'geojsonsf', 'ggmap', 'sf', 'spelling', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

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: 'mvnfast', 'Rfast'

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: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘refund’

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

Package suggested but not available for checking: ‘glmnet’

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

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

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: ‘RSpectra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
Packages required but not available: 'Rcpp', 'geosphere'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘trustOptim’
Error(s) in re-building vignettes:
  ...
--- re-building ‘sparseMVN2.Rmd’ using rmarkdown

Quitting from lines 254-264 [unnamed-chunk-5] (sparseMVN2.Rmd)
Error: processing vignette 'sparseMVN2.Rmd' failed with diagnostics:
there is no package called 'trustOptim'
--- failed re-building ‘sparseMVN2.Rmd’

SUMMARY: processing the following file failed:
  ‘sparseMVN2.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘Rcpp’
Packages required but not available: 'Rcpp', 'glmnet', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘huge’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FactoMineR', 'plotly', 'shiny', 'shinydashboard', 'shinyjs',
  'shinyjqui', 'shinythemes', 'explor', 'shinyWidgets', 'ks',
  'leaflet', 'ape', 'ade4', 'shinycssloaders'

Package suggested but not available for checking: ‘sf’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'plotly', 'reshape', 'gstat', 'fda', 'sf', 'fda.usc'

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

Package suggested but not available for checking: ‘INLA’

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

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

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

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

Package suggested but not available for checking: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'sf', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SpatialExperiment', 'reshape2', 'reticulate', 'keras', 'tensorflow',
  'ggpubr', 'scran', 'scuttle'

Packages suggested but not available for checking:
  'DelayedMatrixStats', 'bluster'

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

Packages suggested but not available for checking:
  'spdep', 'ks', 'caret', 'gstat', 'units', 'lwgeom', 'geodata'

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

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

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

Package suggested but not available for checking: ‘spelling’

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

Package suggested but not available for checking: ‘INLA’

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

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

Package suggested but not available for checking: ‘optimization’

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

Package suggested but not available for checking: ‘tmap’

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: 'ranger', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ICSNP', 'MNM'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘qpdf’

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

Packages suggested but not available for checking: 'lwgeom', 'cartography'

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

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spdep', 'GWmodel', 'plm', 'spatialreg'

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

Packages suggested but not available for checking:
  'RSpectra', 'tmap', 'spam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourvalues', 'leafem', 'leafgl', 'leaflet', 'Rcpp', 'sf', 'tmap',
  'units'

Packages suggested but not available for checking: 'automap', 'gstat'

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

Package suggested but not available for checking: ‘lwgeom’

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

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

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

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

Packages suggested but not available for checking:
  'reshape2', 'gstat', 'raster'

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

Packages suggested but not available for checking:
  'colourvalues', 'geojsonsf', 'jsonify', 'sfheaders'

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:
  'spTimer', 'fields', 'V8'

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

Package suggested but not available for checking: ‘SeuratObject’

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: 'fields', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'adehabitatHR', 'sf', 'units'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.univar',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Skipping checking math rendering: package 'V8' unavailable
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Skipping checking math rendering: package 'V8' unavailable
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.sparse',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘glmnet’

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'fields', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'raster', 'sf', 'trip'
Running ‘testthat.R’ [18s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spbabel)
  > 
  > test_check("spbabel")
  Failed with error:  'there is no package called 'sf''
  Failed with error:  'there is no package called 'sf''
  Failed with error:  'there is no package called 'trip''
  Failed with error:  'there is no package called 'raster''
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 30 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-spFromTable.R:60:3'
  • requireNamespace("raster") is not TRUE (1): 'test-utils.R:2:1'
  • requireNamespace("sf") is not TRUE (2): 'test-sf.R:2:1',
    'test-sfFromTable.R:2:1'
  • requireNamespace("trip") is not TRUE (1): 'test-trip.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-spFromTable.R:73:1'): (code run outside of `test_that()`) ──────
  <packageNotFoundError/error/condition>
  Error in `library(raster)`: there is no package called 'raster'
  Backtrace:
      ▆
   1. ├─base::suppressPackageStartupMessages(library(raster)) at test-spFromTable.R:73:1
   2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
   3. └─base::library(raster)
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 30 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'units', 'sf', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'fields', 'RcppArmadillo'

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

Package suggested but not available for checking: ‘womblR’

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

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

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 checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘womblR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'sf', 'spDataLarge', 'spdep', 'spatialreg'
Packages required but not available: 'rcarbon', 'raster', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'units', 's2'

Packages suggested but not available for checking:
  'spatialreg', 'dbscan', 'RSpectra', 'tmap', 'spam', 'rgeoda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppSpdlog’

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

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘scRNAseq’
Package required but not available: ‘quarto’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fixest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'imager', 'mrbsizeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Ckmeans.1d.dp', 'Seurat'

Package suggested but not available for checking: ‘SeuratObject’

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

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

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

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

Package suggested but not available for checking: ‘caret’

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

Packages suggested but not available for checking: 'calendR', 'lutz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NMF', 'plotly', 'plyr', 'hNMF'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking: 'CVXR', 'clusterSim'

VignetteBuilder package required for checking but not installed: ‘CVXR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rgee', 'geojsonio', 'sf', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'chromote', 'gghighlight', 'ggrepel', 'ggtext', 'gt', 'openxlsx',
  'pagedown', 'shiny', 'shinyalert', 'shinydashboard', 'shinyFeedback',
  'shinyjs', 'shinyWidgets', 'spsComps', 'waiter', 'webshot2'

Package suggested but not available for checking: ‘magick’

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: ‘lomb’

Package suggested but not available for checking: ‘qs’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘raster’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'tm', 'pdftools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'phyloseq', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hunspell’

Package suggested but not available for checking: ‘pdftools’

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

Package suggested but not available for checking: ‘gstat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ranger’
Package suggested but not available for checking: ‘AER’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SpeTestNP.Rmd’ using rmarkdown

Quitting from lines 368-378 [unnamed-chunk-4] (SpeTestNP.Rmd)
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there is no package called 'AER'
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SUMMARY: processing the following file failed:
  ‘SpeTestNP.Rmd’

Error: Vignette re-building failed.
Execution halted
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    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
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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’
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checkRd: (-1) ds_aat.Rd:16: Lost braces
    16 | \doi{10.1111/add.14071}{Boffo et al., 2018}. Participants were presented stimuli from a "test"
       |                        ^
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    16 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
checkRd: (-1) ds_iat.Rd:19: Lost braces
    19 | \doi{10.1016/j.tate.2019.102887}{Abacioglu and colleagues (2019)}. 
       |                                 ^
checkRd: (-1) ds_rapi.Rd:15: Lost braces
    15 | problems within the last year (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989}).
       |                                                                             ^
checkRd: (-1) ds_sst.Rd:17: Lost braces
    17 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
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    22 | \doi{10.1111/acer.12853}{(Pronk, Deursen, Beraha, Larsen, & Wiers, 2015)}.
       |                         ^
checkRd: (-1) splithalfr.Rd:15: Lost braces
    15 |   \item \code{vignette("rapi_sum")} Sum-score for data of the 23-item version of the Rutgers Alcohol Problem Index (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989})
       |                                                                                                                                                                  ^
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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’
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Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
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checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                   ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                              ^
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    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                                             ^
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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’
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checkRd: (-1) vol.m3.Rd:21: Lost braces in \itemize; meant \describe ?
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   248 | and code{port} arguments of sqldf.
       |         ^
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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.
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
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    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
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    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
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    67 |     \code{intermed}}{ - a logical variable denoting whether the intermediate 
       |                     ^
checkRd: (-1) squarem.Rd:134: Lost braces
   134 |       along with the corresponding log-likelihood value.  When the code{objfn} is not specified it will return the fixed-point residual instead of the objective function values. 
       |                                                                        ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'shinydashboard'

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.
checkRd: (-1) plot.SRCS.Rd:48-50: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
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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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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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checkRd: (-1) sscor.Rd:33: Lost braces; missing escapes or markup?
    33 | Otherwise, if {pdim=TRUE}, the pxp SSCM is computed, and then from the SSCM an estimator of the correlation matrix, which is done by the function \code{\link{SSCM2Shape}}, see there for details.
       |               ^
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Running examples in ‘ssc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coBC
> ### Title: CoBC method
> ### Aliases: coBC
> 
> ### ** Examples
> 
> 
> library(ssc)
> 
> ## Load Wine data set
> data(wine)
> 
> cls <- which(colnames(wine) == "Wine")
> x <- wine[, -cls] # instances without classes
> y <- wine[, cls] # the classes
> x <- scale(x) # scale the attributes
> 
> ## Prepare data
> set.seed(20)
> # Use 50% of instances for training
> tra.idx <- sample(x = length(y), size = ceiling(length(y) * 0.5))
> xtrain <- x[tra.idx,] # training instances
> ytrain <- y[tra.idx]  # classes of training instances
> # Use 70% of train instances as unlabeled set
> tra.na.idx <- sample(x = length(tra.idx), size = ceiling(length(tra.idx) * 0.7))
> ytrain[tra.na.idx] <- NA # remove class information of unlabeled instances
> 
> # Use the other 50% of instances for inductive testing
> tst.idx <- setdiff(1:length(y), tra.idx)
> xitest <- x[tst.idx,] # testing instances
> yitest <- y[tst.idx] # classes of testing instances
> 
> ## Example: Training from a set of instances with 1-NN as base classifier.
> set.seed(1)
> m1 <- coBC(x = xtrain, y = ytrain, 
+            learner = caret::knn3, 
+            learner.pars = list(k = 1),
+            pred = "predict")
Error in loadNamespace(x) : there is no package called ‘caret’
Calls: coBC ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
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Package suggested but not available for checking: ‘spelling’

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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  'spThin', 'leaflet', 'sdm'

Package suggested but not available for checking: ‘shinyFiles’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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Packages suggested but not available for checking: 'extraDistr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MESS’

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

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httpuv’
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sship)
  > 
  > test_check("sship")
  [ FAIL 3 | WARN 1 | SKIP 0 | PASS 32 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dec.R:15:1'): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'httpuv'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-dec.R:15:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-enc.R:8:1'): (code run outside of `test_that()`) ───────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'httpuv'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-enc.R:8:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-misc.R:6:3'): an rsa key pair can be made ──────────────────────
  Error in `keygen(directory = tempdir())`: Key files exists! If you really want to overwrite existing files, please set the function argument 'overwrite_existing' to TRUE. Terminating.
  Backtrace:
      ▆
   1. ├─testthat::expect_message(keygen(directory = tempdir())) at test-misc.R:6:3
   2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─sship::keygen(directory = tempdir())
  
  [ FAIL 3 | WARN 1 | SKIP 0 | PASS 32 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘spelling’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'netmeta', 'plyr', 'RevEcoR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qvalue’

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

Packages suggested but not available for checking:
  'caret', 'tidymodels', 'C50', 'factoextra', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘sampleSelection’
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 103-109 [unnamed-chunk-2] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'sampleSelection'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'dbscan', 'DescTools', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sampleSelection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘qpdf’
Packages required but not available: 'sf', 'spmodel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'rstan', 'sf', 'SSN2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'SSN2'

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: ‘gganimate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RDS’

Package suggested but not available for checking: ‘densEstBayes’

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scanstatistics’
Package required but not available: ‘caret’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'shiny', 'shinyjs', 'shinyWidgets'
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'bigstep', 'caret', 'lme4', 'recipes', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'stability', 'shiny', 'shinyBS', 'shinydashboardPlus'

Package suggested but not available for checking: ‘shinytest2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘libstable4u’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mcmcse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'glmnet', 'hdi'
checkRd: (-1) stabsel_parameters.Rd:42: Lost braces
    42 |     always use code{"none"}.}
       |                    ^
checkRd: (-1) stabsel_stabsel.Rd:25: Lost braces
    25 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pROC’

Package suggested but not available for checking: ‘msaenet’

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

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

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

Packages suggested but not available for checking: 'ranger', 'workflowsets'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pool’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'spdep', 'lwgeom', 'geosphere'

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

Package suggested but not available for checking: ‘lme4’

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

Packages suggested but not available for checking: 'afex', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fst’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RcppEigen’

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

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

Package suggested but not available for checking: ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RNifti’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pdftools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'geoTS', 'trend', 'mapview'

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

Package suggested but not available for checking: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'AER', 'censReg', 'dynlm', 'erer', 'lme4', 'plm', 'sampleSelection',
  'spdep', 'survey'
checkRd: (-1) stargazer.Rd:229: Lost braces
   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
checkRd: (-1) stargazer.Rd:246: Lost braces
   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘spdep’

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

Package which this enhances but not available for checking: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'corrr', 'shiny', 'shinyjs', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pander’
Error(s) in re-building vignettes:
  ...
--- re-building ‘starschemar.Rmd’ using rmarkdown

Quitting from lines 173-174 [unnamed-chunk-2] (starschemar.Rmd)
Error: processing vignette 'starschemar.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘starschemar.Rmd’

--- re-building ‘v10_transformation_op.Rmd’ using rmarkdown
--- finished re-building ‘v10_transformation_op.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'sf', 'stars', 'nngeo', 'units'

Package suggested but not available for checking: ‘raster’

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

Packages suggested but not available for checking:
  'OpenStreetMap', 'cubble', 'exactextractr', 'ggforce', 'gstat',
  'lwgeom', 'ncdfgeom', 'plm', 'raster', 'starsdata', 'terra',
  'tsibble'

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

Packages suggested but not available for checking:
  'leaflet.extras', 'mapview', 'magick', 'shiny'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'bigmemory', 'multiApply', 's2dv', 'ClimProjDiags'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'lessR'

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

Packages suggested but not available for checking: 'car', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'qs', 'qpdf', 'DT'

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 suggested but not available for checking: ‘spelling’
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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: ‘DT’
Error(s) in re-building vignettes:
  ...
--- re-building ‘differences-gw-cow.Rmd’ using rmarkdown
--- finished re-building ‘differences-gw-cow.Rmd’

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

Quitting from lines 21-23 [setup] (statelists.Rmd)
Error: processing vignette 'statelists.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘statelists.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'drc', 'car', 'drcte'

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

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

Package suggested but not available for checking: ‘asreml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'animation', 'factoextra', 'ggforce', 'LMMsolver', 'reshape2',
  'spam', 'SpATS'

Package suggested but not available for checking: ‘asreml’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'statgenGWAS', 'LMMsolver', 'spam', 'statgenIBD'

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

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

Package suggested but not available for checking: ‘asreml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rARPACK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lutz’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'ergm.ego', 'EpiModel', 'networksis', 'ndtv'
Packages required but not available: 'shiny', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidytext', 'wordcloud'

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: ‘shiny’

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

Packages suggested but not available for checking:
  'leaflet', 'geojsonsf', 'tmap', 'pct', 'osmdata'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'afex', 'BayesFactor', 'PMCMRplus', 'WRS2'

Packages suggested but not available for checking:
  'metaBMA', 'metaplus', 'rstantools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydisconnect', 'car', 'DDoutlier', 'energy', 'reshape2'

Packages suggested but not available for checking:
  'DescTools', 'reticulate', 'semPlot', 'FactoMineR',
  'FactoInvestigate', 'factoextra', 'onewaytests'

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GGally', 'reshape2', 'ggrepel', 'pROC', 'factoextra', 'pvca',
  'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘VCA’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘drgee’

Package suggested but not available for checking: ‘AF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘drgee’

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

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

Package suggested but not available for checking: ‘energy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'TMB', 'sf', 'fmesher', 'RcppEigen'

Package suggested but not available for checking: ‘hawkesbow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) keypoints.Rd:35-36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:37-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:40-44: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:45-48: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:49-50: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:63-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:66-67: Lost braces in \enumerate; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'MCMCglmm', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'spelling'
Packages required but not available: 'FD', 'ade4', 'geometry', 'ape'

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

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

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qpdf’

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

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

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

Package suggested but not available for checking: ‘swCRTdesign’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggrepel', 'flextable', 'shiny', 'ggcorrplot', 'summarytools',
  'shinythemes', 'DT', 'shinycssloaders', 'shinyjs'

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

Package suggested but not available for checking: ‘reshape2’

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

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

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

Package suggested but not available for checking: ‘mvnfast’

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

Package suggested but not available for checking: ‘fields’

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: 'shiny', 'Rcpp', 'svgViewR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reticulate’
checkRd: (-1) docker_config_collection.Rd:11: Lost braces; missing escapes or markup?
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
checkRd: (-1) docker_container.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
checkRd: (-1) docker_image_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
checkRd: (-1) docker_plugin_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
checkRd: (-1) docker_service_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
checkRd: (-1) docker_task.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
Packages required but not available: 'arm', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'fda', 'raster', 'rasterVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘metR’

Package suggested but not available for checking: ‘sf’

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘xslt’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Ryacas’

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

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

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: 'forecast', 'nnfor'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stm', 'ggraph', 'ggrepel', 'shiny', 'shinyBS', 'shinydashboard',
  'shinyjs', 'DT', 'huge'

Package suggested but not available for checking: ‘quanteda’

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

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

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: ‘reshape2’

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

Packages suggested but not available for checking:
  'geometry', 'huge', 'Rtsne', 'spelling', 'tm', 'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggfittext’

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

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: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

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: 'dvmisc', 'Rcpp'

Package suggested but not available for checking: ‘pander’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'smacofx', 'cordillera', 'energy', 'minerva', 'smacof'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'quanteda', 'spelling'
Malformed Title field: should not end in a period.
Packages required but not available: 'leaflet', 'rworldmap', 'sf', 'terra'

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: ‘imager’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘urltools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'geosphere', 'lwgeom', 'nabor', 'od', 'Rcpp', 'sf', 'sfheaders'

Packages suggested but not available for checking:
  'cyclestreets', 'dodgr', 'leaflet', 'mapsapi', 'opentripplanner',
  'osrm', 'pct', 'rsgeo', 'tmap'

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:
  'interp', 'extraDistr', 'Rcpp', 'RcppArmadillo', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'ks', 'terra', 'raster', 'SiMRiv', 'geosphere', 'leaflet',
  'gstat', 'otuSummary'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) powderymildew.Rd:14-16: Lost braces
    14 | \code{$demographic.coord}{
       |                          ^
checkRd: (-1) powderymildew.Rd:18-20: Lost braces
    18 | \code{$genetic.coord}{
       |                      ^
checkRd: (-1) powderymildew.Rd:22-24: Lost braces
    22 | \code{$demographic.measures}{
       |                             ^
checkRd: (-1) powderymildew.Rd:26-28: Lost braces
    26 | \code{$genetic.frequencies}{
       |                            ^
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'shiny', 'shinyFiles', 'shinyjs', 'DT', 'flextable', 'plotly'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'optmatch', 'glmnet'
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘myNewStrat.R’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘StrathE2E2examples’
checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:79: Lost braces; missing escapes or markup?
    79 | {Parameter estimation:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:88: Lost braces; missing escapes or markup?
    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:98: Lost braces; missing escapes or markup?
    98 | {Compare model runs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:105: Lost braces; missing escapes or markup?
   105 | {Fishery yield analysis:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:111: Lost braces; missing escapes or markup?
   111 | {Visualize model inputs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:117: Lost braces; missing escapes or markup?
   117 | {Visualize model outputs:} \cr
       | ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

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

Packages suggested but not available for checking: 'BART', 'pROC'

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.
Package required but not available: ‘mc2d’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘admtools’

Package suggested but not available for checking: ‘spelling’

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 checking math rendering: package 'V8' unavailable
Packages required but not available: 'ape', 'phangorn', 'ggtree'

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: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘samr’
Packages required but not available: 'Ckmeans.1d.dp', 'Seurat', 'SPECK'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'sf', 'devtools', 'ggrepel'
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                   ^
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                                                      ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘streamDAG.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/streamDAG.Rcheck/vign_test/streamDAG/vignettes/streamDAG_files/figure-html/sp1-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 104179 bytes
Input file size = 104401 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 82401
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 82401

Output IDAT size = 82401 bytes (21778 bytes decrease)
Output file size = 82479 bytes (21922 bytes = 21.00% decrease)


Quitting from lines 142-154 [sp2] (streamDAG.Rmd)
Error: processing vignette 'streamDAG.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘streamDAG.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘suntools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stream’

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

Package suggested but not available for checking: ‘animation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ndjson’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'reticulate', 'osmdata', 'quickPWCR', 'mapview',
  'SuperpixelImageSegmentation', 'OpenImageR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘drc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘qs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘from-base.Rmd’ using rmarkdown

Quitting from lines 31-67 [stringr-base-r-diff] (from-base.Rmd)
Error: processing vignette 'from-base.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘from-base.Rmd’

--- re-building ‘regular-expressions.Rmd’ using rmarkdown
--- finished re-building ‘regular-expressions.Rmd’

--- re-building ‘stringr.Rmd’ using rmarkdown
--- finished re-building ‘stringr.Rmd’

SUMMARY: processing the following file failed:
  ‘from-base.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘faraway’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘stripless_vignette.Rmd’ using rmarkdown

Quitting from lines 108-111 [unnamed-chunk-4] (stripless_vignette.Rmd)
Error: processing vignette 'stripless_vignette.Rmd' failed with diagnostics:
object 'hsb' not found
--- failed re-building ‘stripless_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘caret’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ShortRead’

Package suggested but not available for checking: ‘STRaitRazoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gtsummary’

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

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

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

Package suggested but not available for checking: ‘demography’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'dynlm'
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'car', 'dynlm', 'bfast'

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

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

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

Package suggested but not available for checking: ‘tm’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'ggmap', 'gstat', 'stars'

Package suggested but not available for checking: ‘units’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘quanteda’

Package suggested but not available for checking: ‘devtools’

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.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) subdetect-package.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subdetect-package.Rd:12: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'shiny', 'DT', 'shinyjs', 'colourpicker', 'ranger',
  'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arm', 'caret', 'glmnet', 'ipred', 'SIS'
Package required but not available: ‘ggvis’

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: 'GSVA', 'ChemmineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'geosphere', 'rmapshaper', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ozmaps', 'sf', 'ggiraph', 'usmap', 'geosphere'
Running examples in ‘sugarglider-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_glyph_ribbon
> ### Title: Create a Glyph Ribbon plot using ggplot2
> ### Aliases: geom_glyph_ribbon
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> 
> # Basic glyph map with base map and custom theme
> aus_temp |>
+   ggplot(aes(x_major = long, y_major = lat,
+          x_minor = month, ymin_minor = tmin, ymax_minor = tmax)) +
+   geom_sf(data = ozmaps::abs_ste, fill = "grey95",
+           color = "white",inherit.aes = FALSE) +
+   geom_glyph_ribbon() +
+   ggthemes::theme_map()
Error in loadNamespace(x) : there is no package called ‘ozmaps’
Calls: geom_sf ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples.Rmd’ using rmarkdown

Quitting from lines 21-35 [setup] (Examples.Rmd)
Error: processing vignette 'Examples.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘Examples.Rmd’

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

Quitting from lines 21-33 [setup] (sugarglider.Rmd)
Error: processing vignette 'sugarglider.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘sugarglider.Rmd’

SUMMARY: processing the following files failed:
  ‘Examples.Rmd’ ‘sugarglider.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
Packages suggested but not available for checking: 'plotly', 'tsibble'
Running ‘testthat.R’ [6s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sugrrants)
  Loading required package: ggplot2
  > 
  > test_check("sugrrants")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 34 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-calendar.R:124:3'): The tsibble data ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'tsibble'
  Backtrace:
      ▆
   1. ├─hourly_peds %>% ... at test-calendar.R:124:3
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GBJ’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'magick', 'pander', 'pryr', 'rapportools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dreamerr', 'collapse'

Package suggested but not available for checking: ‘fixest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'survey', 'spdep', 'reshape2', 'sf', 'fields', 'terra'

Packages suggested but not available for checking:
  'INLA', 'readstata13', 'rdhs', 'sae', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'pARI', 'ARIbrain', 'RNifti'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘treemap’
checkRd: (-1) sunburst.Rd:30: Lost braces; missing escapes or markup?
    30 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{csvdata}
       |                                ^
checkRd: (-1) sunburst.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{jsondata}{\code{deprecated} use data argument instead; data in nested d3 JSON hierarchy with `{name:...,  children:[];}`}
       |                                                                                                     ^
checkRd: (-1) sund2b.Rd:22: Lost braces; missing escapes or markup?
    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'terra', 'raster', 'cartogram', 'packcircles', 'rmapshaper',
  'spdep', 'Rcpp', 'automap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ddiv’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) BiclustSet-class.Rd:19: Lost braces
    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'shiny', 'shinyBS'

Packages suggested but not available for checking: 'fMultivar', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'weights', 'plyr', 'umap', 'Rtsne', 'dbscan'

Packages suggested but not available for checking:
  'scater', 'Seurat', 'bluster', 'velocyto.R'

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

Package suggested but not available for checking: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) plot.Rd:42: Lost braces; missing escapes or markup?
    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
Packages required but not available: 'Rcpp', 'RcppEigen'

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 suggested but not available for checking:
  'arm', 'biglasso', 'bigmemory', 'caret', 'devtools', 'glmnet',
  'ipred', 'KernelKnn', 'ranger', 'SIS'
Running examples in ‘SuperLearner-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SL.biglasso
> ### Title: SL wrapper for biglasso
> ### Aliases: SL.biglasso
> 
> ### ** Examples
> 
> 
> data(Boston, package = "MASS")
> Y = Boston$medv
> # Remove outcome from covariate dataframe.
> X = Boston[, -14]
> 
> set.seed(1)
> 
> # Sample rows to speed up example.
> row_subset = sample(nrow(X), 30)
> 
> # Subset rows and columns & use only 2 folds to speed up example.
> sl = SuperLearner(Y[row_subset], X[row_subset, 1:2, drop = FALSE],
+                   family = gaussian(), cvControl = list(V = 2),
+                   SL.library = "SL.biglasso")
Loading required namespace: biglasso
Failed with error:  ‘there is no package called ‘biglasso’’
Error : loading required package (biglasso) failed
Warning in FUN(X[[i]], ...) : Error in algorithm SL.biglasso 
  The Algorithm will be removed from the Super Learner (i.e. given weight 0) 

Loading required namespace: biglasso
Failed with error:  ‘there is no package called ‘biglasso’’
Error : loading required package (biglasso) failed
Warning in FUN(X[[i]], ...) : Error in algorithm SL.biglasso 
  The Algorithm will be removed from the Super Learner (i.e. given weight 0) 

Error in SuperLearner(Y[row_subset], X[row_subset, 1:2, drop = FALSE],  : 
  All algorithms dropped from library
Execution halted
Package required but not available: ‘mice’

Packages suggested but not available for checking:
  'arm', 'extraTrees', 'glmnet', 'ipred', 'KernelKnn', 'ranger'

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:
  'ClusterR', 'ranger', 'caret', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'lme4'
Packages required but not available:
  'Rcpp', 'OpenImageR', 'RcppArmadillo', 'ClusterR'

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

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RcppZiggurat’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘apollo’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'ape', 'devtools'
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
Packages required but not available: 'ape', 'geiger', 'phytools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

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: ‘learnr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'latticeExtra', 'lme4', 'logistf', 'ks', 'extraDistr', 'flexsurv',
  'rvinecopulib', 'MBESS'

Packages suggested but not available for checking: 'kdecopula', 'cubature'

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: ‘PAsso’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flexsurv’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'animation', 'INLA', 'spdep', 'sf'
Note: skipping ‘twinstim.Rnw’ due to unavailable dependencies: 'sf'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'rstantools', 'Rcpp', 'rstan', 'tidybayes', 'ggdist', 'RcppEigen',
  'StanHeaders'

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: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pec’

Packages suggested but not available for checking:
  'censored', 'flexsurv', 'glmnet', 'ranger', 'reticulate', 'treeshap'

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

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

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

Package suggested but not available for checking: ‘rpms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DT’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'pool', 'quarto', 'shiny', 'shinyjs', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gt’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'survey', 'rdhs', 'SUMMER', 'naniar', 'raster', 'spdep', 'sf'

Packages suggested but not available for checking: 'INLA', 'geodata'

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

Packages suggested but not available for checking: 'AER', 'SUMMER'

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: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'plyr', 'groupdata2', 'Rcpp', 'RcppEigen', 'PoissonBinomial'

Packages suggested but not available for checking:
  'PoissonBinomial', 'gurobi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flexsurv’

Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA', 'rstan'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survminer’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘splines2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'caret', 'flexsurv', 'hdnom', 'glmnetUtils'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survey’
Packages required but not available:
  'shiny', 'shinycssloaders', 'DT', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survminer', 'pec'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'ggtext'

Package suggested but not available for checking: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sf.Rd:66: Lost braces; missing escapes or markup?
    66 | A {data.table} which is stored as an attribute of
       |   ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘haldensify’

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

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survminer’
Error(s) in re-building vignettes:
  ...
--- re-building ‘survParamSim.Rmd’ using rmarkdown

Quitting from lines 53-58 [plot_raw_data] (survParamSim.Rmd)
Error: processing vignette 'survParamSim.Rmd' failed with diagnostics:
there is no package called 'survminer'
--- failed re-building ‘survParamSim.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'interp', 'metR', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘latticeExtra’

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

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) coxDT.Rd:76: Lost braces; missing escapes or markup?
    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
Packages required but not available: 'mixsqp', 'reshape'

Package suggested but not available for checking: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

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

Package suggested but not available for checking: ‘tsDyn’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘magick’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'rvinecopulib', 'Rcpp', 'univariateML', 'wdm', 'RcppEigen'

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) koInstall.Rd:24: Lost braces; missing escapes or markup?
    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
checkRd: (-1) svKomodo-package.Rd:18: Lost braces; missing escapes or markup?
    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
checkRd: (-1) svKomodo-package.Rd:28: Lost braces; missing escapes or markup?
    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
checkRd: (-1) svKomodo-package.Rd:37: Lost braces; missing escapes or markup?
    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
Package required but not available: ‘VMDecomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘survey’

Packages suggested but not available for checking: 'tidycensus', 'srvyr'

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: ‘spelling’
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘survey’

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'svyVarSel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Packages suggested but not available for checking: 'srvyr', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plumber’
Package required but not available: ‘caret’

Packages suggested but not available for checking:
  'glmnet', 'ModelMetrics', 'plyr', 'pROC', 'recipes', 'reshape2'

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: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geosphere’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rtsne', 'trackdf', 'swaRm', 'geosphere'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fields', 'devtools'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘swdft-intro.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/swdft.Rcheck/vign_test/swdft/vignettes/swdft-intro_files/figure-html/unnamed-chunk-4-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 43302 bytes
Input file size = 43440 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 39957
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 39957

Output IDAT size = 39957 bytes (3345 bytes decrease)
Output file size = 40035 bytes (3405 bytes = 7.84% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/swdft.Rcheck/vign_test/swdft/vignettes/swdft-intro_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10136 bytes
Input file size = 11006 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8861
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8861

Output IDAT size = 8861 bytes (1275 bytes decrease)
Output file size = 8939 bytes (2067 bytes = 18.78% decrease)


Quitting from lines 211-212 [unnamed-chunk-11] (swdft-intro.Rmd)
Error: processing vignette 'swdft-intro.Rmd' failed with diagnostics:
there is no package called 'fields'
--- failed re-building ‘swdft-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘swdft-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Rcpp', 'quanteda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'timetk', 'tidyquant'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘swephRdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'swfscDAS', 'swfscMisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'swfscMisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pdftools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'plyr'

Packages suggested but not available for checking: 'spelling', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'shinyWidgets'
Running examples in ‘swipeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: swipeR
> ### Title: HTML widget displaying a carousel
> ### Aliases: swipeR
> 
> ### ** Examples
> 
> library(swipeR)
> library(htmltools)
> 
> wrapper <- swipeRwrapper(
+   tags$img(src = "https://swiperjs.com/demos/images/nature-1.jpg"),
+   tags$img(src = "https://swiperjs.com/demos/images/nature-2.jpg"),
+   tags$img(src = "https://swiperjs.com/demos/images/nature-3.jpg"),
+   tags$img(src = "https://swiperjs.com/demos/images/nature-4.jpg"),
+   tags$img(src = "https://swiperjs.com/demos/images/nature-5.jpg"),
+   tags$img(src = "https://swiperjs.com/demos/images/nature-6.jpg"),
+   tags$img(src = "https://swiperjs.com/demos/images/nature-7.jpg"),
+   tags$img(src = "https://swiperjs.com/demos/images/nature-8.jpg")
+ )
> 
> swipeR(
+   wrapper, height = "400px", width = "70%", thumbs = TRUE, keyboard = TRUE,
+   on = list(reachEnd = htmlwidgets::JS("function() {alert('the end');}"))
+ )
> 
> # Shiny example ####
> library(swipeR)
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Packages required but not available: 'shiny', 'shinyAce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'hpa', 'mnorm', 'gena', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'ggpubr', 'ggspatial', 'prettymapr', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) hyph.support.en.Rd:19: Lost braces in \itemize; meant \describe ?
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Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
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checkRd: (-1) elliptical.ts.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
Skipping checking math rendering: package 'V8' unavailable
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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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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.
checkRd: (-1) coord2dist.Rd:14: Lost braces; missing escapes or markup?
    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
Skipping checking math rendering: package 'V8' unavailable
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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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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Skipping checking math rendering: package 'V8' unavailable
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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Skipping checking math rendering: package 'V8' unavailable
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  'shiny', 'shinydashboardPlus', 'shinydashboard', 'shinycssloaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'Rdimtools', 'ADMM', 'fda', 'maotai', 'mclustcomp',
  'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CVXR', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Note: skipping ‘table1-examples.Rmd’ due to unavailable dependencies:
  'MatchIt'
Note: skipping ‘table1-latex.Rmd’ due to unavailable dependencies:
  'flextable'
Packages required but not available: 'MOTE', 'mirt', 'plotly', 'kutils'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gt’
Running examples in ‘table.glue-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: format_big
> ### Title: Format values left of decimal
> ### Aliases: format_big
> 
> ### ** Examples
> 
> 
> big_x <- 1234567
> 
> rspec <- format_big(round_spec(), mark = '|', interval = 3)
> 
> table_value(big_x, rspec) # returns "1|234|567"
Error in glue_data(.x = NULL, ..., .sep = .sep, .envir = .envir, .open = .open,  : 
  is.environment(.envir) is not TRUE
Calls: table_value -> <Anonymous> -> glue_data -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘default_rounder.Rmd’ using rmarkdown

Quitting from lines 53-58 [unnamed-chunk-4] (default_rounder.Rmd)
Error: processing vignette 'default_rounder.Rmd' failed with diagnostics:
is.environment(.envir) is not TRUE
--- failed re-building ‘default_rounder.Rmd’

--- re-building ‘table_guide.Rmd’ using rmarkdown

Quitting from lines 19-25 [setup] (table_guide.Rmd)
Error: processing vignette 'table_guide.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘table_guide.Rmd’

SUMMARY: processing the following files failed:
  ‘default_rounder.Rmd’ ‘table_guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
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Packages suggested but not available for checking:
  'reshape2', 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking:
  'shinyWidgets', 'shinyEffects', 'echarts4r'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking:
  'shiny', 'shinyFiles', 'sortable', 'shinyAce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'recipes', 'spelling', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Skipping checking math rendering: package 'V8' unavailable
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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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘DescTools’

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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking: 'forecast', 'spelling'

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', 'FastGP', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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Package suggested but not available for checking: ‘shinydashboard’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking: 'miceadds', 'plyr'

Package which this enhances but not available for checking: ‘LSAmitR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'sf', 'mapiso'

Package suggested but not available for checking: ‘lwgeom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'promises', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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manual.
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Specified C++11: please drop specification unless essential
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'paws.storage', 'qs', 'shiny', 'shinybusy', 'shinyWidgets', 'torch'
Skipping checking math rendering: package 'V8' unavailable
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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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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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manual.
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checkRd: (-1) mean_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
checkRd: (-1) median_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_tbrf.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tbrf.Rcheck/vign_test/tbrf/vignettes/intro_to_tbrf_files/figure-html/unnamed-chunk-5-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28054 bytes
Input file size = 28168 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 23689
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 23689

Output IDAT size = 23689 bytes (4365 bytes decrease)
Output file size = 23767 bytes (4401 bytes = 15.62% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tbrf.Rcheck/vign_test/tbrf/vignettes/intro_to_tbrf_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 8 bits/pixel, 246 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5391 bytes
Input file size = 6219 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5022
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5022

Output IDAT size = 5022 bytes (369 bytes decrease)
Output file size = 5100 bytes (1119 bytes = 17.99% decrease)


Quitting from lines 123-138 [unnamed-chunk-7] (intro_to_tbrf.Rmd)
Error: processing vignette 'intro_to_tbrf.Rmd' failed with diagnostics:
there is no package called 'ggalt'
--- failed re-building ‘intro_to_tbrf.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_to_tbrf.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
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Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'ggpubr', 'golem', 'plotly', 'reshape2', 'rstatix', 'shiny',
  'shinyFeedback', 'shinyjs'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'reshape2'

Package suggested but not available for checking: ‘dearseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'terra', 'geosphere', 'rasterVis', 'raster', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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'LazyData' is specified without a 'data' directory
Packages required but not available:
  'reshape', 'reshape2', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘mrgsolve’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'ggpubr', 'ICSNP', 'geometry', 'DT', 'forecast', 'fmri',
  'extraDistr', 'cubature', 'reshape2', 'interp'

Package suggested but not available for checking: ‘oro.nifti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) windows/tk2reg.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) windows/tk2reg.Rd:18: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) windows/tk2reg.Rd:51: Escaped LaTeX specials: \_
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checkRd: (-1) windows/tk2reg.Rd:60: Escaped LaTeX specials: \_
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Mcomp', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking: 'DT', 'tcpl'

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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  'Rcpp', 'TDAstats', 'T4cluster', 'energy', 'maotai', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking:
  'TDAstats', 'reticulate', 'TDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'TDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CDM’

Packages suggested but not available for checking: 'devtools', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Ecume', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppSimdJson’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘latticeExtra’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'devtools', 'GA'
Dependence on R version ‘4.2.3’ not with patchlevel 0
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘sf’

Package which this enhances but not available for checking: ‘R2wd’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) crossEntropy.Rd:32: Lost braces
    32 | link{squaredError}
       |     ^
Package suggested but not available for checking: ‘shiny’
Error(s) in re-building vignettes:
  ...
--- re-building ‘qenv.Rmd’ using rmarkdown

Quitting from lines 151-184 [unnamed-chunk-10] (qenv.Rmd)
Error: processing vignette 'qenv.Rmd' failed with diagnostics:
there is no package called 'shiny'
--- failed re-building ‘qenv.Rmd’

--- re-building ‘teal-code.Rmd’ using rmarkdown
--- finished re-building ‘teal-code.Rmd’

SUMMARY: processing the following file failed:
  ‘qenv.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘units’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'teal', 'teal.transform', 'tern', 'DT', 'ggrepel', 'shiny',
  'shinyjs', 'shinyvalidate', 'shinyWidgets', 'teal.logger',
  'teal.reporter', 'teal.widgets', 'tern.gee', 'tern.mmrm', 'vistime'

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggmosaic', 'shiny', 'teal', 'teal.transform', 'DT', 'shinyjs',
  'shinyTree', 'shinyvalidate', 'shinyWidgets', 'teal.logger',
  'teal.reporter', 'teal.widgets', 'tern'

Packages suggested but not available for checking:
  'colourpicker', 'ggExtra', 'ggpmisc', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'teal.slice', 'shinyjs', 'teal.logger', 'teal.reporter',
  'teal.widgets'

Package suggested but not available for checking: ‘shinyvalidate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'flextable', 'shiny', 'shinybusy', 'shinyWidgets'

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'shiny', 'shinycssloaders', 'shinyjs', 'shinyWidgets',
  'teal.logger', 'teal.widgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyjs', 'shinyvalidate', 'teal.logger', 'teal.widgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyjs', 'shinyWidgets'

Packages suggested but not available for checking:
  'DT', 'shinytest2', 'shinyvalidate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'smoothr', 'terra'

Packages suggested but not available for checking: 'ggforce', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'fields', 'raster', 'scoringRules', 'reshape2', 'Rcpp',
  'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httpuv’

Packages suggested but not available for checking: 'devtools', 'promises'

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: ‘rerddap’
Packages required but not available: 'bayesm', 'extraDistr'

Package suggested but not available for checking: ‘klaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'wordcloud', 'arulesViz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tsbox’
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > # These tests are more extensive and only need to run on GHA, not on CRAN.
  > library(testthat)
  > library(tempdisagg)
  > 
  > test_check("tempdisagg")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_misc.R:5:1'): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(tsbox)`: there is no package called 'tsbox'
  Backtrace:
      ▆
   1. └─base::library(tsbox) at test_misc.R:5:1
  ── Error ('test_td.R:3:1'): (code run outside of `test_that()`) ────────────────
  <packageNotFoundError/error/condition>
  Error in `library(tsbox)`: there is no package called 'tsbox'
  Backtrace:
      ▆
   1. └─base::library(tsbox) at test_td.R:3:1
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘AICcmodavg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'excursions', 'fMRIscrub', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'ciftiTools', 'RNifti', 'oro.nifti', 'INLA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘V8’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape2', 'plotly'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'terra', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'fICA', 'Rcpp', 'tsBSS', 'ICtest', 'RcppArmadillo'

Package suggested but not available for checking: ‘stochvol’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'TRES', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'reshape2', 'pryr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tensorEVD-documentation.Rmd’ using rmarkdown

Quitting from lines 213-246 [unnamed-chunk-5] (tensorEVD-documentation.Rmd)
Error: processing vignette 'tensorEVD-documentation.Rmd' failed with diagnostics:
incorrect number of dimensions
--- failed re-building ‘tensorEVD-documentation.Rmd’

SUMMARY: processing the following file failed:
  ‘tensorEVD-documentation.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reticulate', 'tfruns', 'tfautograph'

Package suggested but not available for checking: ‘keras3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘glmnet’
Packages required but not available: 'raster', 'gsignal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rainbow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘EpiModel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'discretefit', 'Rcpp'

Package suggested but not available for checking: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcppHungarian', 'shiny'

Packages suggested but not available for checking:
  'colourpicker', 'shinyjs', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tern', 'geeasy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tern', 'mmrm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magick', 'sf', 'terra', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'sf', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MC_CRUDE.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) MC_IS.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) PROB_BASEVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) PROB_DETVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) SORM.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) SYS_LSF-class.Rd:16: Lost braces
    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
Packages required but not available: 'cxhull', 'Rvcg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kairos’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'pdftools'

Packages suggested but not available for checking: 'magick', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mirt', 'shinydashboard', 'shiny', 'DT', 'golem', 'officedown',
  'bruceR', 'openxlsx', 'flextable', 'shinycssloaders', 'difR',
  'lordif', 'latticeExtra', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) lognormConstCVCI.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mice', 'Amelia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘openxlsx’
Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(testdat)
  
  Attaching package: 'testdat'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("testdat")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 182 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-reporter_excel.R:12:3'): excel_results ─────────────────────────
  Error: Package "openxlsx" needed for this function to work.Please install it.
  Backtrace:
      ▆
   1. └─testdat::output_results_excel(x, file_out) at test-reporter_excel.R:12:3
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 182 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'highs', 'gurobi', 'mirt', 'mirtCAT', 'shiny', 'shinythemes',
  'shinyWidgets', 'shinyjs', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'minerva', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ContourFunctions’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'plotly', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'FactoMineR', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'narray', 'imputeTS', 'greybox', 'dqrng', 'Rfast', 'philentropy'

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: ‘fractional’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hunspell’

Package suggested but not available for checking: ‘devtools’

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’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pdftools', 'rjtools'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

Packages suggested but not available for checking: 'pdftools', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘systemfit’

Packages which this enhances but not available for checking:
  'AER', 'alpaca', 'bife', 'brms', 'dynlm', 'feisr', 'fixest',
  'forecast', 'glmmTMB', 'lme4', 'metaSEM', 'miceadds', 'pglm', 'plm',
  'remify', 'remstats', 'remstimate', 'spatialreg', 'spdep'
Packages required but not available: 'text2vec', 'qgraph', 'ClusterR'

Packages suggested but not available for checking: 'tm', 'quanteda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'corpustools', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'rsparse'

Packages suggested but not available for checking: 'udpipe', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) infer_Z.Rd:16: Lost braces; missing escapes or markup?
    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp.Rd:26: Lost braces
    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
checkRd: (-1) sibp.Rd:28: Lost braces; missing escapes or markup?
    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp_amce.Rd:19: Lost braces
    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
Packages required but not available: 'plyr', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'tidytext', 'tm', 'wordcloud', 'plyr', 'udpipe',
  'glmnet', 'pdftools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'text2vec', 'Rcpp', 'RSpectra', 'RcppArmadillo'

Packages suggested but not available for checking:
  'spelling', 'tidytext', 'topicmodels', 'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidytext', 'tm', 'ggwordcloud'

Packages suggested but not available for checking:
  'ggrepel', 'ggpubr', 'ggraph', 'ape', 'topicmodels', 'corrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'udpipe', 'BTM', 'qgraph', 'ggraph', 'ggforce', 'concaveman',
  'ggrepel', 'ggalt', 'uwot'
Packages suggested but not available for checking: 'textreuse', 'udpipe'
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'ggrepel', 'recipes', 'reticulate', 'tune'

Packages suggested but not available for checking:
  'glmnet', 'ranger', 'ggwordcloud', 'osfr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'recipes', 'tokenizers'

Packages suggested but not available for checking:
  'sentencepiece', 'spacyr', 'text2vec', 'tokenizers.bpe', 'udpipe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'Rcpp'

Package suggested but not available for checking: ‘plyr’

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: 'hunspell', 'quanteda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘qvalue’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'tensorflow', 'keras'

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: ‘reticulate’

Package suggested but not available for checking: ‘tensorflow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'tensorflow'

Packages suggested but not available for checking: 'keras3', 'tfestimators'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httpuv', 'reticulate', 'tensorflow'

Packages suggested but not available for checking: 'cloudml', 'pixels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'tensorflow', 'tfruns'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'reticulate', 'tensorflow', 'wav'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'tensorflow'

Packages suggested but not available for checking:
  'tfestimators', 'keras', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reticulate', 'tensorflow', 'tfdatasets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tensorflow', 'keras', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tensorflow', 'reticulate', 'keras'

Package suggested but not available for checking: ‘tfdatasets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘refund’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tfrmt', 'shiny', 'shinyjs', 'DT', 'gt', 'sortable', 'shinyWidgets',
  'shinycssloaders', 'webshot2', 'shinyAce', 'shinyFeedback'

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda.usc', 'tclust', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plumber', 'geojsonsf'

Packages suggested but not available for checking:
  'devtools', 'edgebundle', 'sf', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) shoulders.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'trtf', 'tram'
Note: skipping ‘blood_loss_report.Rnw’ due to unavailable dependencies:
  'trtf', 'tram'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'theft', 'reshape2', 'Rtsne', 'umap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tsibble', 'fabletools', 'tsfeatures', 'feasts', 'Rcatch22',
  'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

Package suggested but not available for checking: ‘gdalcubes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gganimate', 'ggiraph', 'shiny'
Package required but not available: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Running examples in ‘Thermimage-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diffFrame
> ### Title: A frame difference function for subtracting adjacent frames from
> ###   an imported thermal image sequence.
> ### Aliases: diffFrame
> 
> ### ** Examples
> 
> 
> # set w to 640 and h to 480
> w<-640
> h<-480
> f<-system.file("extdata", "SampleSEQ.seq", package = "Thermimage")
> x<-frameLocates(f, w=w, h=h)
> suppressWarnings(templookup<-raw2temp(1:65535))
> alldata<-unlist(lapply(x$f.start, getFrames, vidfile=f, w=w, h=h))
> alldata<-matrix(alldata, nrow=w*h, byrow=FALSE)
> alltemperature<-templookup[alldata]
> alltemperature<-unname(matrix(alltemperature, nrow=w*h, byrow=FALSE))
> 
> dalltemperature<-as.matrix(diffFrame(alltemperature, absolute=TRUE), nrow=w)
> 
> # Plot 
> plotTherm(dalltemperature[,1], templookup=NULL, w=w, h=h,  minrangeset=min(dalltemperature),
+           maxrangeset=max(dalltemperature), trans="mirror.matrix")
Error in loadNamespace(x) : there is no package called ‘fields’
Calls: plotTherm ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'hts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'rvg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'plumber', 'shiny'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
'LazyData' is specified without a 'data' directory
Running examples in ‘thorn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: thorn-shiny
> ### Title: Shiny bindings for 'thorn'
> ### Aliases: thorn-shiny thornOutput renderThorn
> 
> ### ** Examples
> 
> # use a shader as the background of a Shiny app ####
> library(thorn)
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package which this enhances but not available for checking: ‘shiny’
Package required but not available: ‘anytime’

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ade4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pROC', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pROC', 'ThresholdROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'revdbayes', 'rust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking: 'combiter', 'reshape2'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tictactoe)
  > 
  > test_check("tictactoe")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-game.R:3:1'): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(combiter)`: there is no package called 'combiter'
  Backtrace:
      ▆
   1. └─base::library(combiter) at test-game.R:3:1
  ── Error ('test-xhash.R:3:1'): (code run outside of `test_that()`) ─────────────
  <packageNotFoundError/error/condition>
  Error in `library(combiter)`: there is no package called 'combiter'
  Backtrace:
      ▆
   1. └─base::library(combiter) at test-xhash.R:3:1
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘workflowsets’

Packages suggested but not available for checking:
  'recipes', 'multilevelmod', 'censored', 'baguette', 'brulee',
  'rstanarm', 'ranger', 'flexsurv', 'glmnet', 'klaR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggdist’

Packages suggested but not available for checking:
  'rstan', 'rstantools', 'rstanarm', 'MCMCglmm', 'bayesplot', 'brms',
  'ggrepel', 'bindrcpp', 'gganimate', 'transformr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ClusterR', 'autostats'

Packages suggested but not available for checking:
  'arulesCBA', 'embed', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ggforce', 'spelling'
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tidycat.Rcheck/vign_test/tidycat/vignettes/intro_files/figure-html/unnamed-chunk-5-1.png
1152x768 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 24859 bytes
Input file size = 25753 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21774
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 21734
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 21734

Output IDAT size = 21734 bytes (3125 bytes decrease)
Output file size = 21812 bytes (3941 bytes = 15.30% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tidycat.Rcheck/vign_test/tidycat/vignettes/intro_files/figure-html/unnamed-chunk-6-1.png
1152x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 63963 bytes
Input file size = 64125 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 52558
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 52558

Output IDAT size = 52558 bytes (11405 bytes decrease)
Output file size = 52636 bytes (11489 bytes = 17.92% decrease)


Quitting from lines 127-143 [unnamed-chunk-7] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'ggforce'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'cicerone', 'DT', 'GGally', 'ggcorrplot', 'golem', 'gt',
  'IDEAFilter', 'plotly', 'shiny', 'shinyjs', 'shinyWidgets',
  'timevis', 'tippy'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'tigris', 'units'

Packages suggested but not available for checking:
  'survey', 'srvyr', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GA', 'tsibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'tune'

Packages suggested but not available for checking:
  'ClusterR', 'klaR', 'RcppHungarian', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gtsummary’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'GGally', 'MBESS', 'misty'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'validata', 'presenter', 'autostats', 'tidybins', 'Ckmeans.1d.dp'

Packages suggested but not available for checking: 'ggstance', 'EIX'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Rcpp', 'RcppSpdlog'
Package suggested but not available for checking: ‘shiny’
Packages suggested but not available for checking:
  'dann', 'recipes', 'tune'
Running examples in ‘tidydann-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nearest_neighbor_adaptive
> ### Title: Discriminant Adaptive Nearest Neighbor Classification
> ### Aliases: nearest_neighbor_adaptive
> 
> ### ** Examples
> 
> 
> library(parsnip)
> library(tidydann)
> 
> data("two_class_dat", package = "modeldata")
> 
> model <- nearest_neighbor_adaptive(neighbors = 2) |>
+   set_engine("dann") |>
+   fit(formula = Class ~ A + B, data = two_class_dat)
Error in `check_installs()`:
! This engine requires some package installs: 'dann'
Backtrace:
    ▆
 1. ├─generics::fit(...)
 2. └─parsnip::fit.model_spec(...)
 3.   └─parsnip:::check_installs(object)
 4.     └─rlang::abort(...)
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(tidydann)
  > 
  > test_check("tidydann")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 22 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_A_nearest_neighbor_adaptive.R:4:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `library(recipes)`: there is no package called 'recipes'
  Backtrace:
      ▆
   1. ├─base::suppressPackageStartupMessages(library(recipes)) at test_A_nearest_neighbor_adaptive.R:4:1
   2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
   3. └─base::library(recipes)
  ── Error ('test_C_ecosystem.R:8:1'): (code run outside of `test_that()`) ───────
  <packageNotFoundError/error/condition>
  Error in `library(recipes)`: there is no package called 'recipes'
  Backtrace:
      ▆
   1. ├─base::suppressPackageStartupMessages(library(recipes)) at test_C_ecosystem.R:8:1
   2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
   3. └─base::library(recipes)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 22 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘learnr’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘explore’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tidydice.Rmd’ using rmarkdown

Quitting from lines 32-35 [unnamed-chunk-1] (tidydice.Rmd)
Error: processing vignette 'tidydice.Rmd' failed with diagnostics:
there is no package called 'explore'
--- failed re-building ‘tidydice.Rmd’

SUMMARY: processing the following file failed:
  ‘tidydice.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘EdSurvey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking:
  'arm', 'bestglm', 'gaselect', 'glmnet', 'lme4', 'sensitivity',
  'shrinkTVP'
Running examples in ‘tidyfit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: classify
> ### Title: Classification on tidy data
> ### Aliases: classify
> 
> ### ** Examples
> 
> data <- tidyfit::Factor_Industry_Returns
> data <- dplyr::mutate(data, Return = ifelse(Return > 0, 1, 0))
> fit <- classify(data, Return ~ ., m("lasso", lambda = c(0.001, 0.1)), .mask = c("Date", "Industry"))
Error in m("lasso", lambda = c(0.001, 0.1)) : 
  Package 'glmnet' is required for method 'lasso'. Run install.packages('glmnet').
Calls: classify -> m
Execution halted
Package required but not available: ‘fst’

Package suggested but not available for checking: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fst’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'shiny', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fuzzyjoin', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
Packages required but not available: 'anytime', 'tidyRSS', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ape', 'netrankr'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'spelling', 'qpdf'
Packages suggested but not available for checking:
  'devtools', 'estimatr', 'glmnet', 'nprobust'
Running examples in ‘tidyhte-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HTE_cfg
> ### Title: Configuration of Quantities of Interest
> ### Aliases: HTE_cfg
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `HTE_cfg$new`
> ## ------------------------------------------------
> 
> mcate_cfg <- MCATE_cfg$new(cfgs = list(x1 = KernelSmooth_cfg$new(neval = 100)))
Error in soft_require("nprobust") : The package "nprobust" is required.
Calls: <Anonymous> ... <Anonymous> -> initialize -> soft_require -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘experimental_analysis.Rmd’ using rmarkdown

Quitting from lines 93-107 [recipe] (experimental_analysis.Rmd)
Error: processing vignette 'experimental_analysis.Rmd' failed with diagnostics:
The package "nprobust" is required.
--- failed re-building ‘experimental_analysis.Rmd’

--- re-building ‘methodological_details.Rmd’ using rmarkdown

Quitting from lines 147-153 [cfg] (methodological_details.Rmd)
Error: processing vignette 'methodological_details.Rmd' failed with diagnostics:
The package "nprobust" is required.
--- failed re-building ‘methodological_details.Rmd’

--- re-building ‘observational_analysis.Rmd’ using rmarkdown

Quitting from lines 86-104 [recipe] (observational_analysis.Rmd)
Error: processing vignette 'observational_analysis.Rmd' failed with diagnostics:
The package "nprobust" is required.
--- failed re-building ‘observational_analysis.Rmd’

SUMMARY: processing the following files failed:
  ‘experimental_analysis.Rmd’ ‘methodological_details.Rmd’
  ‘observational_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tsibble’

Packages suggested but not available for checking: 'lmomco', 'SPEI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'listviewer', 'wordcloud'
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                           ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-tidyjson.Rmd’ using rmarkdown
--- finished re-building ‘introduction-to-tidyjson.Rmd’

--- re-building ‘visualizing-json.Rmd’ using rmarkdown

Quitting from lines 64-78 [unnamed-chunk-2] (visualizing-json.Rmd)
Error: processing vignette 'visualizing-json.Rmd' failed with diagnostics:
there is no package called 'wordcloud'
--- failed re-building ‘visualizing-json.Rmd’

SUMMARY: processing the following file failed:
  ‘visualizing-json.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'mvrsquared', 'Rcpp', 'tidytext', 'RcppArmadillo'

Packages suggested but not available for checking:
  'quanteda', 'tm', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pdftools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘units’
Package suggested but not available for checking: ‘tidytext’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tidylo.Rmd’ using rmarkdown
Warning: code chunks must not depend on the uncached chunk "bigram_counts"

Quitting from lines 37-50 [bigram_counts] (tidylo.Rmd)
Error: processing vignette 'tidylo.Rmd' failed with diagnostics:
there is no package called 'tidytext'
--- failed re-building ‘tidylo.Rmd’

SUMMARY: processing the following file failed:
  ‘tidylo.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘MplusAutomation’

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'recipes', 'tune', 'workflowsets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'corrr', 'FactoMineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggstance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyplus)
  > 
  > test_check("tidyplus")
  Coalesced 'x' from: 'x'
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 124 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-replace-na-if.R:10:3', 'test-unite-str.R:47:3'
  • get unite_str working with symbol! (1): 'test-unite-str.R:11:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-unite-str.R:81:3'): unite_str matches new sf as string ─────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'sf'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-unite-str.R:81:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 124 ]
  Deleting unused snapshots:
  • replace-na-if/works.csv
  • unite-str/notremove.csv
  Error: Test failures
  Execution halted
Package required but not available: ‘tokenizers’

Packages suggested but not available for checking: 'europepmc', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstanarm', 'tune', 'workflowsets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Cubist', 'ranger'
Error(s) in re-building vignettes:
  ...
--- re-building ‘cubist.Rmd’ using rmarkdown

Quitting from lines 11-18 [setup] (cubist.Rmd)
Error: processing vignette 'cubist.Rmd' failed with diagnostics:
there is no package called 'Cubist'
--- failed re-building ‘cubist.Rmd’

--- re-building ‘glm.Rmd’ using rmarkdown
--- finished re-building ‘glm.Rmd’

--- re-building ‘lm.Rmd’ using rmarkdown
--- finished re-building ‘lm.Rmd’

--- re-building ‘mars.Rmd’ using rmarkdown
--- finished re-building ‘mars.Rmd’

--- re-building ‘non-r.Rmd’ using rmarkdown
--- finished re-building ‘non-r.Rmd’

--- re-building ‘ranger.Rmd’ using rmarkdown

Quitting from lines 11-21 [unnamed-chunk-1] (ranger.Rmd)
Error: processing vignette 'ranger.Rmd' failed with diagnostics:
there is no package called 'ranger'
--- failed re-building ‘ranger.Rmd’

--- re-building ‘regression.Rmd’ using rmarkdown
--- finished re-building ‘regression.Rmd’

--- re-building ‘rf.Rmd’ using rmarkdown
--- finished re-building ‘rf.Rmd’

--- re-building ‘save.Rmd’ using rmarkdown
--- finished re-building ‘save.Rmd’

--- re-building ‘sql.Rmd’ using rmarkdown
--- finished re-building ‘sql.Rmd’

--- re-building ‘tree.Rmd’ using rmarkdown
--- finished re-building ‘tree.Rmd’

--- re-building ‘xgboost.Rmd’ using rmarkdown
--- finished re-building ‘xgboost.Rmd’

SUMMARY: processing the following files failed:
  ‘cubist.Rmd’ ‘ranger.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘timetk’

Packages suggested but not available for checking:
  'alphavantager', 'tibbletime', 'Rblpapi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'rgee', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘anytime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

Packages suggested but not available for checking: 'C50', 'Cubist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidymodels', 'spatialsample', 'maxnet', 'recipes', 'sf', 'terra',
  'tune', 'workflowsets'

Packages suggested but not available for checking:
  'blockCV', 'pastclim', 'ranger', 'rgbif', 'spelling', 'stacks',
  'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'OpenMx', 'blavaan', 'MplusAutomation', 'dbscan', 'car'

Packages suggested but not available for checking:
  'tidyLPA', 'umx', 'dagitty', 'mice', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ttservice', 'SeuratObject', 'Seurat', 'plotly'

Packages suggested but not available for checking: 'GGally', 'SingleR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'MatchIt', 'spelling'
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'ape', 'bioseq', 'seqinr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesFactor', 'lme4', 'lmerTest', 'afex', 'MEMSS'
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
generate_control.html:87:1 (generate_control.Rd:36): Warning: trimming empty <li>
generate_control.html:86:1 (generate_control.Rd:36): Warning: trimming empty <ol>
generate_weights.html:220:1 (generate_weights.Rd:102): Warning: trimming empty <li>
generate_weights.html:219:1 (generate_weights.Rd:102): Warning: trimming empty <ol>
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'terra'

Packages suggested but not available for checking: 'maptiles', 'metR', 's2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tokenizers’

Packages suggested but not available for checking:
  'hunspell', 'quanteda', 'reshape2', 'stm', 'tm', 'topicmodels',
  'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidybayes’

Package suggested but not available for checking: ‘BART’

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: 'fuzzyjoin', 'sf', 'tigris'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘feather’
Packages suggested but not available for checking: 'nlmixr2', 'shiny'
Package required but not available: ‘pool’

Packages suggested but not available for checking: 'spelling', 'odbc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'piton'

Package suggested but not available for checking: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'shinyjs'
Package required but not available: ‘alakazam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rcbalance’

Package suggested but not available for checking: ‘rrelaxiv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Packages suggested but not available for checking: 'leaflet', 'tidycensus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'nanotime', 'spdl', 'RcppInt64'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lwgeom', 'sf', 'smoothr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

Packages suggested but not available for checking: 'leaflet', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'miniUI', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘prodlim’
Packages required but not available: 'magick', 'pdftools'

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: 'cheapr', 'collapse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mets’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘openxlsx’
checkRd: (-1) setup_sql_functions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
checkRd: (-1) setup_sql_functions.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
checkRd: (-1) setup_sql_grant_rights.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
checkRd: (-1) setup_sql_grant_rights.Rd:17: Lost braces; missing escapes or markup?
    17 | Grant execute on {timeseriesdb} functions
       |                  ^
checkRd: (-1) setup_sql_tables.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
checkRd: (-1) setup_sql_tables.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
checkRd: (-1) setup_sql_triggers.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
Package required but not available: ‘ggfittext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'recipes', 'plotly', 'padr', 'anytime', 'forecast', 'tsfeatures'

Packages suggested but not available for checking:
  'modeltime', 'glmnet', 'tune'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) POSIXst-class.Rd:247: Lost braces
   247 |   do any conversion on the POSIX{l,c}t objects).
       |                                 ^
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘shinydisconnect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'ggiraph'

Packages suggested but not available for checking: 'openxlsx', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘xslt’

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: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'clusterProfiler', 'survminer'

Packages suggested but not available for checking:
  'AnnoProbe', 'FactoMineR', 'factoextra', 'ggpubr', 'Rtsne'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘collapse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'altdoc', 'tinysnapshot'
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

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:
  'marginaleffects', 'quarto', 'tinysnapshot', 'webshot2'
Running ‘tinytest.R’ [1s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("tinytable")
  + }
  
  test-assert.R.................    0 tests    
  test-assert.R.................    0 tests    
  test-assert.R.................    1 tests [0;32mOK[0m 
  test-assert.R.................    2 tests [0;32mOK[0m [0;34m0.3s[0m
  
  test-colrowspan.R.............    0 tests    Error: Package tinysnapshot could not be loaded
  Execution halted
Package suggested but not available for checking: ‘hrbrthemes’
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++14: please drop specification unless essential
Package required but not available: ‘RBesT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'mniw'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'Rcpp', 'rstan', 'ggpubr', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'rstantools', 'sf', 'leaflet', 'tmap', 'spam', 'spdep',
  'shinythemes', 'shinyFeedback', 'shinybusy', 'shinyWidgets',
  'shinyjs', 'bayesplot', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape’
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ReDaMoR', 'shiny', 'shinydashboard', 'DT', 'jsonvalidate',
  'promises'

Packages suggested but not available for checking: 'RClickhouse', 'BED'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘huge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'tableone', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'lmomco'

Package suggested but not available for checking: ‘Lmoments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'tmaptools', 'sf', 'stars', 'units', 'leaflet', 'leafsync', 'leafem'

Packages suggested but not available for checking:
  'rmapshaper', 'cartogram', 'osmdata', 'shiny', 's2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'lwgeom', 'stars', 'units'

Packages suggested but not available for checking:
  'tmap', 'rmapshaper', 'osmdata', 'OpenStreetMap', 'raster', 'shiny',
  'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppEigen’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'Rcpp', 'TMB', 'StanHeaders', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tm’
checkRd: (-1) tv_episode_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘reshape2’
Running examples in ‘Tmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_na
> ### Title: Plot missing data
> ### Aliases: gg_na
> 
> ### ** Examples
> 
> # What a mess. 
> # Feature 10 is missing a lot. Observations 25 and 35 are completely missing.
> # Most of features 40-45 are missing, except for the first few observations.
> set.seed(2016-07-12)
> x <- matrix(1, nrow=50, ncol=50)
> x[sample(prod(dim(x)), 100)] <- NA
> x <- data.frame(x)
> x$X10[sample(length(x$X10), 25)] <- NA
> x[c(25, 35), ] <- NA
> x[1:40, 40:45] <- NA
> gg_na(x)
Error: ggplot2 and reshape2 packages needed for this function to work. Please install them.
Execution halted
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'phangorn', 'ape', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tagcloud', 'ggrepel'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'pdftools', 'Rcampdf', 'tm.lexicon.GeneralInquirer'

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’

Package suggested but not available for checking: ‘dexterMST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vcr', 'devtools'
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(TNRS)
  > 
  > 
  > test_check("TNRS")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TNRS.Rcheck/tests/testthat/setup-tnrs.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("TNRS")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-tnrs.R:14:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Packages suggested but not available for checking: 'devtools', 'ggalt'
Error(s) in re-building vignettes:
  ...
--- re-building ‘visualization-cookbook.Rmd’ using rmarkdown

Quitting from lines 38-50 [load_packages] (visualization-cookbook.Rmd)
Error: processing vignette 'visualization-cookbook.Rmd' failed with diagnostics:
there is no package called 'ggalt'
--- failed re-building ‘visualization-cookbook.Rmd’

SUMMARY: processing the following file failed:
  ‘visualization-cookbook.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'shiny', 'shinyWidgets'

Package suggested but not available for checking: ‘apexcharter’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

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: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'ggpubr', 'ggcorrplot', 'ggforce', 'UpSetR',
  'randomcoloR', 'EnhancedVolcano', 'GGally', 'survminer', 'Rtsne',
  'umap', 'clusterProfiler', 'enrichplot', 'WGCNA', 'factoextra',
  'ggrepel', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'geojsonsf', 'tidycensus', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
Packages required but not available: 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'latticeExtra', 'lhs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pander’
checkRd: (-1) Data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:17: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Arothron', 'alphashape3d', 'compositions', 'morphomap', 'Rvcg',
  'Morpho', 'oce', 'geometry', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) getSegsExtra.Rd:14: Lost braces
    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘topicmodels’

Package suggested but not available for checking: ‘stm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

Packages suggested but not available for checking:
  'udpipe', 'word2vec', 'uwot', 'ggrepel', 'ggalt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gdistance', 'plotly', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRbase', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'torch', 'torchvision'

Package suggested but not available for checking: ‘tokenizers’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘katex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'torch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

Package suggested but not available for checking: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'caret', 'glmnet'
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'tm', 'quanteda'

Packages suggested but not available for checking: 'toscaData', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'hdi', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bibliometrix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggdist’

Packages suggested but not available for checking:
  'car', 'afex', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘TreeTools’

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'energy', 'plotly'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘regtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available:
  'DT', 'leaflet', 'shiny', 'shinydashboard', 'shinyAce',
  'shinycssloaders'

Packages suggested but not available for checking: 'tcpl', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cicerone', 'DT', 'flextable', 'ggiraph', 'shiny', 'shinycssloaders',
  'shinydisconnect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pcalg’

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.
Package required but not available: ‘MESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘openxlsx’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘etm’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'reshape', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'keras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NMdata', 'flextable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'netmeta', 'nmadb'
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'ape', 'hunspell', 'phangorn', 'reshape2', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'adehabitatHR', 'geosphere', 'move', 'raster', 'sf'

Package suggested but not available for checking: ‘adehabitatLT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'Rcpp', 'shiny', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'adehabitatLT', 'move', 'ctmm', 'moveHMM', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'pagedown', 'vcr'
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trackdown)
  > 
  > test_check("trackdown")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/trackdown.Rcheck/tests/testthat/setup-trackdown.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("trackdown")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-trackdown.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Packages required but not available:
  'trackeR', 'plotly', 'DT', 'shiny', 'shinyjs', 'shinydashboard',
  'shinyWidgets', 'sf', 'mapdeck', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'fda', 'leaflet', 'ggmap'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

Package suggested but not available for checking: ‘onion’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RNifti’

Packages suggested but not available for checking: 'mmand', 'divest'

Package which this enhances but not available for checking: ‘oro.nifti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fixest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘competitiontoolbox’
checkRd: (-1) Sim-Functions.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:100-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:109-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:114-116: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'DescriptiveStats.OBeu'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'adabag', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geosphere’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'FD', 'TPD'
checkRd: (-1) trait_missing.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
Error(s) in re-building vignettes:
  ...
--- re-building ‘traitstrap-workflow.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/traitstrap.Rcheck/vign_test/traitstrap/vignettes/traitstrap-workflow_files/figure-html/plot-raw-dist-np-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44342 bytes
Input file size = 44480 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 39512
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 39512

Output IDAT size = 39512 bytes (4830 bytes decrease)
Output file size = 39590 bytes (4890 bytes = 10.99% decrease)


Quitting from lines 377-395 [multivariate-prep] (traitstrap-workflow.Rmd)
Error: processing vignette 'traitstrap-workflow.Rmd' failed with diagnostics:
there is no package called 'FD'
--- failed re-building ‘traitstrap-workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘traitstrap-workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'OpenStreetMap', 'adehabitatLT', 'forecast', 'taxidata', 'sf'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'tram', 'mlt', 'cotram', 'dHSIC', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'tram', 'mlt', 'TMB', 'coneproj', 'RcppEigen'

Packages suggested but not available for checking:
  'lme4', 'gamm4', 'glmmTMB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tram', 'CVXR', 'mlrMBO', 'mlt', 'lhs', 'smoof'

Packages suggested but not available for checking:
  'penalized', 'glmnet', 'trtf', 'tbm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mlt’

Packages suggested but not available for checking:
  'trtf', 'lme4', 'merDeriv', 'latticeExtra', 'mlt.docreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tram', 'cotram'

Packages suggested but not available for checking:
  'abess', 'tramnet', 'mlt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stars', 'sf', 'units'

Package suggested but not available for checking: ‘elevatr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Tlasso', 'HeteroGGM', 'dcov', 'huge'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |        ^
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |                                         ^
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking: 'animation', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'starnet', 'joinet'

Packages suggested but not available for checking:
  'glmtrans', 'xrnet', 'ecpc', 'fwelnet', 'palasso', 'devtools', 'CVXR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Tlasso’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DescTools’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(transx)
  > 
  > test_check("transx")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-outliers.R:8:3'): winsorize ────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'DescTools'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(out_winsorise(x), DescTools::Winsorize(x)) at test-outliers.R:8:3
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 115 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘plyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘trapezoid.Rnw’ using Sweave
Loading required package: trapezoid
Loading required package: plyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘plyr’
Loading required package: ggplot2

Error: processing vignette 'trapezoid.Rnw' failed with diagnostics:
 chunk 4 (label = generalizedTrapezoids) 
Error in ldply(arguments, function(z) { : could not find function "ldply"

--- failed re-building ‘trapezoid.Rnw’

SUMMARY: processing the following file failed:
  ‘trapezoid.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'terra', 'sf', 'elevatr'
Package required but not available: ‘RProtoBuf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinydashboard'

Packages suggested but not available for checking:
  'Eunomia', 'DatabaseConnector', 'CohortGenerator', 'webshot2',
  'plotly', 'Capr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Packages required but not available: 'ape', 'dispRity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rayvertex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

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: 'reshape2', 'phyloseq', 'ape'

Package suggested but not available for checking: ‘adaptiveGPCA’

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adjclust', 'csaw', 'InteractionSet', 'reshape2', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlpack', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'shiny', 'shinyjs', 'TreeTools', 'Rcpp'

Packages suggested but not available for checking:
  'hypervolume', 'kdensity', 'phangorn', 'plotly', 'Quartet', 'Rcpp',
  'Rogue', 'spelling', 'Ternary', 'TreeDistData', 'TreeSearch',
  'Umatrix', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Seurat', 'plotly', 'qpdf'
Running examples in ‘treefit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_n_arms_star_data
> ### Title: Generate a multi-dimensional star tree data
> ### Aliases: generate_n_arms_star_data
> 
> ### ** Examples
> 
> # Generate a 100-dimensional star tree data that contain 500 data points
> # and fit a star tree with 3 arms. The generated data are a bit noisy but
> # tree-like.
> star100.tree_like <- treefit::generate_n_arms_star_data(100, 500, 3, 0.1)
> # Reduce dimension to visualize.
> star3.tree_like = prcomp(star100.tree_like, rank.=3)$x
> plotly::plot_ly(data.frame(star3.tree_like),
+                 x=~PC1,
+                 y=~PC2,
+                 z=~PC3,
+                 type="scatter3d",
+                 mode="markers",
+                 marker=list(size=1))
Error in loadNamespace(x) : there is no package called ‘plotly’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggfittext’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ape', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'promises', 'Rcpp', 'Rogue', 'shiny', 'shinyjs', 'TreeDist',
  'TreeTools'

Packages suggested but not available for checking:
  'phangorn', 'Quartet', 'shinytest', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'TreeSim', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'geiger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'sf'

Packages suggested but not available for checking: 'devtools', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'ade4', 'adegenet', 'adegraphics', 'distory', 'fields',
  'phangorn', 'phytools', 'Rcpp', 'RLumShiny', 'shiny', 'shinyBS'

Packages suggested but not available for checking:
  'pander', 'reshape2', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phytools', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ape'

Packages suggested but not available for checking:
  'phyloTop', 'DDD', 'geiger', 'nLTT', 'castor', 'adephylo', 'picante',
  'treebalance', 'RPANDA', 'RSpectra', 'abcrf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp'

Package suggested but not available for checking: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp'

Packages suggested but not available for checking:
  'spelling', 'phangorn', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'plotly', 'shiny'
Running examples in ‘trelliscopejs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cog
> ### Title: Cast Column as a Cognostic
> ### Aliases: cog
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(tidyr)
> library(purrr)
> library(ggplot2)
> library(plotly)
Error in library(plotly) : there is no package called ‘plotly’
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trelliscopejs)
  > 
  > test_check("trelliscopejs")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-trelliscope.R:8:3'): examples run without barfing ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(plotly)`: there is no package called 'plotly'
  Backtrace:
      ▆
   1. ├─base::suppressPackageStartupMessages(library(plotly)) at test-trelliscope.R:8:3
   2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
   3. └─base::library(plotly)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘trending’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ciTools’

Packages suggested but not available for checking: 'brms', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'plyr', 'Rssa', 'imputeTS'

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘gtrendsR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ManifoldOptim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tlars', 'glmnet'

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'Rcpp', 'parglm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'tidybayes', 'StanHeaders',
  'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggtern', 'shiny'

Packages suggested but not available for checking:
  'sf', 'leaflet', 'httpuv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'bayesplot', 'RcppEigen', 'StanHeaders'

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: ‘GA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'DT', 'factoextra', 'ggcorrplot', 'ggpubr', 'shiny',
  'shinydashboardPlus', 'shinydashboard', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ez'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape’
Error(s) in re-building vignettes:
  ...
--- re-building ‘trinROC_vignette.Rmd’ using rmarkdown

Quitting from lines 15-24 [setup] (trinROC_vignette.Rmd)
Error: processing vignette 'trinROC_vignette.Rmd' failed with diagnostics:
there is no package called 'reshape'
--- failed re-building ‘trinROC_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘trinROC_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'plyr'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rcbalance', 'rlemon', 'optmatch'

Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'traipse'

Packages suggested but not available for checking:
  'adehabitatLT', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'pROC', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'spelling', 'readstata13', 'pdftools'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'reshape2', 'GA', 'propagate'

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘minqa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlt', 'tram'

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: ‘hdrcde’

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.
Package required but not available: ‘survPen’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spacefillr', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hdm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘anytime’

Packages suggested but not available for checking:
  'forecast', 'tsibble', 'tsibbledata', 'tibbletime', 'units',
  'imputeTS', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ICtest', 'BSSprep', 'Rcpp', 'forecast', 'RcppArmadillo'

Packages suggested but not available for checking:
  'stochvol', 'MTS', 'tsbox'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'ranger'

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rvinecopulib', 'kdensity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'keras', 'tensorflow', 'reticulate', 'tsutils'

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.
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘TSclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'TMB', 'mev', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) binary_transform.Rd:16: Lost braces; missing escapes or markup?
    16 | Converts any variable with two possible values to a {0,1} binary
       |                                                     ^
checkRd: (-1) binary_transform.Rd:13: Lost braces; missing escapes or markup?
    13 | A vector with values in {0,1}.
       |                         ^
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘rugarch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigmemory', 'caret', 'pryr', 'synchronicity', 'wdm'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RcppRoll', 'ranger', 'glmnet', 'Cubist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'wordcloud', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'cubature', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lbfgsb3c', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'forecast', 'RcppRoll'

Packages suggested but not available for checking: 'Mcomp', 'GGally'

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: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'TMB', 'Rcpp', 'flextable', 'tsdistributions', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggforce', 'timetk'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsgc_vignette.Rmd’ using rmarkdown

Quitting from lines 16-34 [setup] (tsgc_vignette.Rmd)
Error: processing vignette 'tsgc_vignette.Rmd' failed with diagnostics:
there is no package called 'ggforce'
--- failed re-building ‘tsgc_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘tsgc_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tsibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘anytime’

Packages suggested but not available for checking: 'nanotime', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'shiny', 'tsibble'

Package suggested but not available for checking: ‘fabletools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MAPA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'keras', 'tensorflow', 'tsutils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'keras', 'tensorflow', 'tsutils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tensorflow', 'keras', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'gdtools', 'raster', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggdist', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'forecast', 'DescTools', 'hht', 'daltoolbox'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'EMD', 'ModelMetrics', 'RSNNS', 'Rlibeemd', 'elmNNRcpp',
  'plyr', 'keras', 'tfdatasets'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'textTinyR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dsa', 'tsbox'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bfast', 'RcppRoll'

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'forecast', 'forecastHybrid', 'plotly', 'reshape2', 'tsibble'

Packages suggested but not available for checking:
  'devtools', 'DT', 'UKgrid'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'flextable', 'car', 'ks'

Packages suggested but not available for checking:
  'tsdistributions', 'tsgarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'openxlsx', 'reshape2'
Packages required but not available: 'forecast', 'MAPA'

Package suggested but not available for checking: ‘thief’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Running examples in ‘TSVC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TSVC
> ### Title: Tree-Structured Modelling of Varying Coefficients
> ### Aliases: TSVC print.TSVC
> 
> ### ** Examples
> 
> # Swiss Labour Market 
> library(AER)
Error in library(AER) : there is no package called ‘AER’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'plotly', 'shiny', 'miniUI', 'forecast', 'shinyhelper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PolynomF', 'nnfor', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape', 'stlplus', 'wql'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'sf', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking: 'pbkrtest', 'lme4'
Package required but not available: ‘rstpm2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ddalpha', 'bfp', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pbkrtest', 'lme4'

Package suggested but not available for checking: ‘reshape2’

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.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘klaR’
Packages required but not available: 'ranger', 'mlrMBO', 'lhs', 'smoof'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GPfit', 'recipes'

Packages suggested but not available for checking:
  'C50', 'censored', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggpol’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'learnr', 'parsermd', 'shiny'

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘DescToolsAddIns’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'systemfit', 'bvarsv', 'plm'

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: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_tvtools.Rmd’ using knitr
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.


Quitting from lines 20-21 [unnamed-chunk-2] (Introduction_to_tvtools.Rmd)
Error: processing vignette 'Introduction_to_tvtools.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘Introduction_to_tvtools.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_to_tvtools.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Rcpp', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'twang', 'latticeExtra', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'latticeExtra'

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.
checkRd: (-1) tweedie-internal.Rd:74: Lost braces
    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘V8’

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: 'Rcpp', 'RcppEigen'

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:
  'plyr', 'quanteda', 'quanteda.textstats', 'topicmodels', 'stm',
  'leaflet', 'ldatuning', 'tm'

Packages suggested but not available for checking: 'tidytext', 'servr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'tidytext'

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
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tmle’

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fixest’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'onewaytests', 'car'

Package suggested but not available for checking: ‘WRS2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'hal9001', 'haldensify'

Package suggested but not available for checking: ‘ranger’

Package which this enhances but not available for checking: ‘sl3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) cambodia.Rd:47: Lost braces
    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) microdata.Rd:33: Lost braces
    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) u5mr_cohort.Rd:111: Lost braces
   111 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'geosphere', 'exifr', 'link2GI', 'terra', 'concaveman',
  'spatialEco'

Package suggested but not available for checking: ‘mapview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GA', 'hyper2', 'Rdimtools', 'shiny'

Packages suggested but not available for checking:
  'caret', 'DT', 'glmnet', 'GSelection', 'plyr', 'shinyalert',
  'shinyBS', 'shinyjs', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'flextable', 'onbrand', 'shiny'

Packages suggested but not available for checking:
  'GA', 'GGally', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'automap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'unmarked', 'Rcpp', 'RSpectra', 'rstan', 'rstantools',
  'RcppArmadillo', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking: 'raster', 'terra'

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: 'cppRouting', 'fields', 'sf', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'tsibble', 'tsoutliers', 'ggforce', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'shiny'

Packages suggested but not available for checking:
  'DT', 'ggrepel', 'ggstatsplot', 'plotly', 'plyr', 'Rtsne',
  'survminer', 'umap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DT', 'shiny', 'shinydashboard'
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘topicmodels’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'esemifar', 'rugarch', 'smoots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'pander', 'plyr'

Packages suggested but not available for checking: 'car', 'GGally', 'MBESS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘collapse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘xaringan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘questionr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tsibble’

Packages suggested but not available for checking: 'devtools', 'TSstudio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
Packages suggested but not available for checking: 'leaflet', 'sf'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'tidytext', 'hunspell', 'tm', 'raster', 'sf', 'quanteda', 'spacyr'

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: ‘clusterSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'Rcpp', 'RSpectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'shiny', 'shinyjs', 'reshape2', 'fields', 'plyr', 'geometry',
  'AdaptGauss', 'DataVisualizations'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'plotly', 'shiny', 'shinydashboard', 'shinyFiles',
  'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mc2d’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'OpenMx', 'hrbrthemes', 'openxlsx'

Packages suggested but not available for checking: 'devtools', 'spelling'

Package which this enhances but not available for checking: ‘DiagrammeRsvg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'echarts4r', 'gt', 'leaflet', 'leaflet.extras', 'plotly',
  'treemap', 'ggspatial', 'ggrepel', 'gtExtras', 'sf'

Package suggested but not available for checking: ‘magick’

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: ‘spelling’
Packages required but not available: 'mvnfast', 'GGally', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggtext', 'ggrepel'

Package suggested but not available for checking: ‘treemapify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘compositions’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rstan’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'terrainr', 'terra', 'sf'
Package suggested but not available for checking: ‘geometry’
Error(s) in re-building vignettes:
  ...
--- re-building ‘convexhull.Rmd’ using rmarkdown

Quitting from lines 41-44 [unnamed-chunk-2] (convexhull.Rmd)
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
there is no package called 'geometry'
--- failed re-building ‘convexhull.Rmd’

SUMMARY: processing the following file failed:
  ‘convexhull.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'magick', 'ggpubr', 'alakazam', 'gprofiler2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

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: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'lme4', 'Rcpp', 'TMB', 'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking:
  'raster', 'shiny', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bayesplot’
Error(s) in re-building vignettes:
  ...
--- re-building ‘unmconf.Rmd’ using rmarkdown

Quitting from lines 67-90 [unnamed-chunk-2] (unmconf.Rmd)
Error: processing vignette 'unmconf.Rmd' failed with diagnostics:
there is no package called 'bayesplot'
--- failed re-building ‘unmconf.Rmd’

SUMMARY: processing the following file failed:
  ‘unmconf.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘huge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tidyxl', 'DT'
Running ‘testthat.R’ [11s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(unpivotr)
  > 
  > test_check("unpivotr")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 256 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-enhead.R:310:3'): the `drop` argument works ────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'tidyxl'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-enhead.R:310:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 256 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘html.Rmd’ using rmarkdown
--- finished re-building ‘html.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 147-172 [tidyxl-unpivotr-demo] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'tidyxl'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘small-multiples.Rmd’ using rmarkdown

Quitting from lines 39-45 [unnamed-chunk-2] (small-multiples.Rmd)
Error: processing vignette 'small-multiples.Rmd' failed with diagnostics:
there is no package called 'tidyxl'
--- failed re-building ‘small-multiples.Rmd’

SUMMARY: processing the following files failed:
  ‘introduction.Rmd’ ‘small-multiples.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
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.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'cubature', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixtools', 'reshape2', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pgdraw', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘adespatial’
Packages required but not available: 'openxlsx', 'tidytext', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'sampleSelection', 'mvProbit'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ExtendedAppendix.Rnw’ using knitr
--- finished re-building ‘ExtendedAppendix.Rnw’

--- re-building ‘Manuscript.Rnw’ using knitr

Quitting from lines 159-160 [dataLoad] (Manuscript.Rnw)
Error: processing vignette 'Manuscript.Rnw' failed with diagnostics:
there is no package called 'sampleSelection'
--- failed re-building ‘Manuscript.Rnw’

SUMMARY: processing the following file failed:
  ‘Manuscript.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'miniUI'

Package suggested but not available for checking: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'triebeard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'raster', 'fasterize', 'shiny', 'leaflet', 'leafem', 'leafpop',
  'geojsonsf', 'magick', 'terra', 'stars', 'vapour', 'gdalraster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spelling', 'sf', 'USA.state.boundaries.data'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘openxlsx’

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: ‘sf’
Running examples in ‘usdata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: us_temp
> ### Title: US Temperature Data
> ### Aliases: us_temp
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> library(maps)
> library(sf)
Error in library(sf) : there is no package called ‘sf’
Execution halted
Packages required but not available: 'terra', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'spelling', 'tsibble'
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘precrec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'recipes', 'tune'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'magick', 'spelling'
Package suggested but not available for checking: ‘plotly’
Running examples in ‘USgas-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: usgas
> ### Title: US Monthly Consumption of Natural Gas by End Use
> ### Aliases: usgas
> ### Keywords: datasets gas natural state timeseries us
> 
> ### ** Examples
> 
> 
> library(plotly)
Error in library(plotly) : there is no package called ‘plotly’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 79-92 [unnamed-chunk-5] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tsibble’

Packages suggested but not available for checking: 'devtools', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GGally’
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘usmapdata’

Packages suggested but not available for checking:
  'ggrepel', 'sf', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'Phase123', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mldr’

Package suggested but not available for checking: ‘C50’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Cubist', 'forecast', 'ipred', 'ranger', 'vctsfr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'RcppAnnoy', 'RSpectra', 'dqrng'

Packages suggested but not available for checking:
  'bigstatsr', 'RcppHNSW', 'rnndescent'

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: 'ggpubr', 'survML', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'prospectr', 'photobiology'

Packages suggested but not available for checking: 'mrgsolve', 'learnr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
Package suggested but not available for checking: ‘tm’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘gamm4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'leaflet', 'ggspatial', 'geojsonio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Package required but not available: ‘listviewer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pyMTurkR', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsdmx’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reticulate', 'plotly', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'devtools', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'leaflet', 'devtools', 'h3jsr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EFA.MRFA', 'fungible', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Seurat', 'SeuratObject', 'sctransform'
Packages required but not available: 'urltools', 'sf', 'geojsonsf'

Package suggested but not available for checking: ‘lwgeom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plm', 'rstatix', 'ggrepel', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'latticeExtra', 'Rcpp'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppEigen’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'MTS', 'sparsevar', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) vardannual.Rd:97: Lost braces
    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
checkRd: (-1) vardannual.Rd:99: Lost braces
    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
checkRd: (-1) vardcrospoor.Rd:122: Lost braces
   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
checkRd: (-1) vardcrospoor.Rd:124: Lost braces
   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
checkRd: (-1) vardom_othstr.Rd:69: Lost braces
    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
checkRd: (-1) varpoord.Rd:121: Lost braces
   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) betaburr.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
checkRd: (-1) betafrechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
checkRd: (-1) kumburr7.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'SAM', 'caret', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘energy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ranger’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(varImp)
  Loading required package: measures
  Loading required package: party
  Loading required package: grid
  Loading required package: mvtnorm
  Loading required package: modeltools
  Loading required package: stats4
  Loading required package: strucchange
  Loading required package: zoo
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  Loading required package: sandwich
  > 
  > test_check("varImp")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_base.R:42:3'): varImp functions ────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(ranger)`: there is no package called 'ranger'
  Backtrace:
      ▆
   1. └─base::library(ranger) at test_base.R:42:3
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘gstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘jmcm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Boruta', 'caret'
Error(s) in re-building vignettes:
  ...
--- re-building ‘varrank.Rmd’ using knitr
** Processing: figure/unnamed-chunk-4-1.png
432x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29516 bytes
Input file size = 29630 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 25252
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 25252

Output IDAT size = 25252 bytes (4264 bytes decrease)
Output file size = 25330 bytes (4300 bytes = 14.51% decrease)


Quitting from lines 79-91 [unnamed-chunk-5] (varrank.Rmd)
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building ‘varrank.Rmd’

SUMMARY: processing the following file failed:
  ‘varrank.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'shiny', 'RcppArmadillo'

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) Acoef_sh.Rd:23: Lost braces; missing escapes or markup?
    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lmeresampler', 'merDeriv', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'lhs', 'mlrMBO', 'smoof', 'spam'

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'RcppEnsmallen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) decomposition.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
checkRd: (-1) moving.estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'VFP', 'STB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mosum’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'effects', 'plyr', 'car', 'AER'
checkRd: (-1) datasets.Rd:15: Lost braces
    15 | and dimension information (\code{dim} or code{length}) of each item,
       |                                              ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp'

Packages suggested but not available for checking:
  'adegenet', 'poppr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'geojsonio', 'sf', 'shiny'
Running examples in ‘vchartr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vchart-shiny
> ### Title: Shiny bindings for vchart
> ### Aliases: vchart-shiny vchartOutput renderVchart
> 
> ### ** Examples
> 
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

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: ‘Ecdat’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'crul', 'webmockr', 'urltools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'forecast', 'Mcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘geomorph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘vcvComp-worked-example.Rmd’ using rmarkdown

Quitting from lines 46-54 [GPA] (vcvComp-worked-example.Rmd)
Error: processing vignette 'vcvComp-worked-example.Rmd' failed with diagnostics:
there is no package called 'geomorph'
--- failed re-building ‘vcvComp-worked-example.Rmd’

SUMMARY: processing the following file failed:
  ‘vcvComp-worked-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'drc', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘compositions’

Package suggested but not available for checking: ‘ggtern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lhs’
Running examples in ‘vdg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sampler
> ### Title: Sampler Function
> ### Aliases: sampler
> 
> ### ** Examples
> 
> ## Default spherical design region
> set.seed(1896)
> samp1 <- sampler(n = 100, design = expand.grid(x = -1:1, y = -1:1))
> plot(samp1)
> 
> ## Supplying a custom sampling function based on lhs::improvedLHS()
> library("lhs")
Error in library("lhs") : there is no package called ‘lhs’
Execution halted
Specified C++11: please drop specification unless essential
Packages required but not available: 'ggpubr', 'ggtext', 'plyr'

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pander', 'reshape2', 'qgraph'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'GpGp', 'GPvecchia', 'TruncatedNormal', 'RcppArmadillo'

Package suggested but not available for checking: ‘lhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'plotly', 'DT'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'biwavelet', 'spam', 'fields', 'Rcpp'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘swephR’

Packages suggested but not available for checking: 'qpdf', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'spelling', 'listviewer', 'V8', 'learnr', 'shiny'
Running examples in ‘vegawidget-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: image
> ### Title: Create or write image
> ### Aliases: image vw_to_svg vw_to_bitmap vw_write_svg vw_write_png
> 
> ### ** Examples
> 
>   # call any of these functions using either a vegaspec or a vegawidget
>   svg <- vw_to_svg(vegawidget(spec_mtcars))
Error: Package(s): "V8" needed for this function to work. Please install.
Execution halted
Package required but not available: ‘plyr’

Packages suggested but not available for checking: 'labdsv', 'interp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'taxlist', 'vegdata'

Packages suggested but not available for checking: 'biblio', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘QCA’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘collapse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ciftiTools', 'plotly', 'reticulate'

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: ‘oro.nifti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'flexdashboard', 'httpuv', 'keras', 'luz',
  'paws.machine.learning', 'plotly', 'plumber', 'ranger', 'recipes',
  'reticulate', 'smdocker', 'stacks', 'tensorflow', 'torch'
Packages required but not available: 'lme4', 'lmerTest'

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: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘VCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'lme4', 'RcppEigen'

Package suggested but not available for checking: ‘gKRLS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘seqinr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ape', 'seqinr'
Running examples in ‘vhica-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CUB
> ### Title: Computes the Codon Usage Bias of DNA sequences
> ### Aliases: CUB
> 
> ### ** Examples
> 
> 	seq.file <- system.file("extdata/Genes", "Amd.fas", package="vhica")
> 	CUB(seq.file)
Error in CUB(seq.file) : Reading FASTA files require package seqinr
Execution halted
Package required but not available: ‘crul’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'terra', 'sf'
checkRd: (-1) VirtualArray-single-bracket-method.Rd:6: Lost braces
     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
Running examples in ‘via-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RasterArray-class
> ### Title: Array of "SpatRaster"-class objects
> ### Aliases: RasterArray-class RasterArray
> 
> ### ** Examples
> 
> # example data
>   ex <- rastex()
Error in rastex() : This function requires the 'terra' package.
Execution halted
Running ‘tinytest.R’ [1s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > if (requireNamespace("tinytest", quietly=TRUE)){
  + 	tinytest::test_package("via")
  + }
  
  test_RasterArray_base.R.......    0 tests    Error in library(terra) : there is no package called 'terra'
  Calls: <Anonymous> ... eval -> source -> withVisible -> eval -> eval -> library
  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:
  'DT', 'ggpubr', 'shiny', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'mapview', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) vietnamcode.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:16: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyjs', 'shinythemes', 'shinyWidgets', 'shinydashboard',
  'golem', 'JBrowseR', 'DT', 'ggpubr', 'plotly', 'reshape2', 'hidecan'

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'sf', 'terra', 'ForestTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'leaflet', 'plotly'
Error(s) in re-building vignettes:
  ...
--- re-building ‘example-boltzman-wealth.Rmd’ using rmarkdown

Quitting from lines 18-21 [setup] (example-boltzman-wealth.Rmd)
Error: processing vignette 'example-boltzman-wealth.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building ‘example-boltzman-wealth.Rmd’

--- re-building ‘extending-agents.Rmd’ using rmarkdown

Quitting from lines 18-21 [setup] (extending-agents.Rmd)
Error: processing vignette 'extending-agents.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building ‘extending-agents.Rmd’

--- re-building ‘extending-resources.Rmd’ using rmarkdown

Quitting from lines 18-20 [setup] (extending-resources.Rmd)
Error: processing vignette 'extending-resources.Rmd' failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘extending-resources.Rmd’

SUMMARY: processing the following files failed:
  ‘example-boltzman-wealth.Rmd’ ‘extending-agents.Rmd’
  ‘extending-resources.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'glmnet', 'ranger'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'ranger', 'knockoff'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'Rcpp', 'ranger'

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: 'shiny', 'kdecopula'
Running examples in ‘VineCopula-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BiCopKDE
> ### Title: Kernel estimate of a Bivariate Copula Density
> ### Aliases: BiCopKDE
> 
> ### ** Examples
> 
> # simulate data from Joe copula
> cop <- BiCop(3, tau = 0.3)
> u <- BiCopSim(1000, cop)
> contour(cop)  # true contours
> 
> # kernel contours with standard normal margins
> BiCopKDE(u[, 1], u[, 2])
Error in BiCopKDE(u[, 1], u[, 2]) : 
  The 'kdecopula' package must be installed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'rvinecopulib', 'kde1d', 'Rcpp', 'RcppEigen', 'wdm'

Package suggested but not available for checking: ‘AppliedPredictiveModeling’

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 suggested but not available for checking:
  'DT', 'fastshap', 'NeuralNetTools'

Packages which this enhances but not available for checking:
  'C50', 'caret', 'Cubist', 'glmnet', 'mixOmics', 'ranger', 'RSNNS',
  'tidymodels'
Packages required but not available: 'applicable', 'recipes'

Package suggested but not available for checking: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'recipes', 'tune', 'workflowsets'

Packages suggested but not available for checking:
  'baguette', 'Cubist', 'glmnet', 'ranger', 'viraldomain'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recipes’

Package suggested but not available for checking: ‘Cubist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rmgarch', 'BigVAR', 'ks', 'matlib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) viridis.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:24-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:45: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘terra’
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survminer’
Packages required but not available:
  'terra', 'ade4', 'rnaturalearth', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘odbc’

Packages suggested but not available for checking: 'jsonld', 'spelling'

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: 'ggpmisc', 'reshape2'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Running examples in ‘VisCollin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biomass
> ### Title: Biomass Production in the Cape Fear Estuary
> ### Aliases: biomass
> ### Keywords: dataset
> 
> ### ** Examples
> 
> data(biomass)
> str(biomass)
'data.frame':	45 obs. of  17 variables:
 $ loc    : Factor w/ 3 levels "OI","SI","SM": 1 1 1 1 1 1 1 1 1 1 ...
 $ type   : Factor w/ 3 levels "DVEG","SHRT",..: 1 1 1 1 1 2 2 2 2 2 ...
 $ biomass: int  676 516 1052 868 1008 436 544 680 640 492 ...
 $ H2S    : int  -610 -570 -610 -560 -610 -620 -590 -610 -580 -610 ...
 $ sal    : int  33 35 32 30 33 33 36 30 38 30 ...
 $ Eh7    : int  -290 -268 -282 -232 -318 -308 -264 -340 -252 -288 ...
 $ pH     : num  5 4.75 4.2 4.4 5.55 5.05 4.25 4.45 4.75 4.6 ...
 $ buf    : num  2.34 2.66 4.18 3.6 1.9 3.22 4.5 3.5 2.62 3.04 ...
 $ P      : num  20.2 15.6 18.7 22.8 37.8 ...
 $ K      : num  1442 1299 1154 1045 522 ...
 $ Ca     : num  2150 1845 1750 1674 3360 ...
 $ Mg     : num  5169 4358 4041 3966 4609 ...
 $ Na     : num  35184 28170 26455 25073 31664 ...
 $ Mn     : num  14.29 7.73 17.81 49.15 30.52 ...
 $ Zn     : num  16.5 14 15.3 17.3 22.3 ...
 $ Cu     : num  5.02 4.19 4.79 4.09 4.6 ...
 $ NH4    : num  59.5 51.4 68.8 82.3 70.9 ...
> biomass.mod <- lm (biomass ~ H2S + sal + Eh7 + pH + buf + P + K + Ca + Mg + Na +
+                            Mn + Zn + Cu + NH4,
+                  data=biomass)
> car::vif(biomass.mod)
Error in loadNamespace(x) : there is no package called ‘car’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggExtra', 'netmeta', 'plyr', 'qgraph', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bayesm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'plotly', 'spelling'
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rssa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'Rcpp', 'rstantools', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking: 'shiny', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'shiny', 'shinyWidgets', 'colourpicker', 'ggraph'
Packages suggested but not available for checking:
  'flextable', 'gt', 'plotly'
Running examples in ‘visOmopResults-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: formatTable
> ### Title: Creates a flextable or gt object from a dataframe
> ### Aliases: formatTable
> 
> ### ** Examples
> 
> # Example 1
> mockSummarisedResult() |>
+   formatEstimateValue(decimals = c(integer = 0, numeric = 1)) |>
+   formatHeader(
+     header = c("Study strata", "strata_name", "strata_level"),
+     includeHeaderName = FALSE
+   ) |>
+   formatTable(
+     type = "flextable",
+     style = "default",
+     na = "--",
+     title = "fxTable example",
+     subtitle = NULL,
+     caption = NULL,
+     groupColumn = "group_level",
+     groupAsColumn = TRUE,
+     groupOrder = c("cohort1", "cohort2"),
+     merge = "all_columns"
+   )
Error in fxTableInternal(x, delim = delim, style = style, na = na, title = title,  : 
  The package "flextable" is required.
Calls: formatTable -> fxTableInternal -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plotly', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘xplorerr’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'oro.dicom', 'shiny', 'shinyjs', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'shinyBS', 'plyr', 'ggrepel', 'DT', 'Rtsne', 'shinybusy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyhelper', 'shinycssloaders', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fable', 'fabletools', 'tsibble'

Packages suggested but not available for checking: 'demography', 'feasts'

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:
  'reshape2', 'ggrepel', 'wpa', 'ggraph', 'tidytext', 'ggwordcloud'

Package suggested but not available for checking: ‘flexdashboard’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'seqinr', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'condvis2', 'GGally', 'ggalt'

Packages suggested but not available for checking:
  'tidymodels', 'lemon', 'ranger', 'caret', 'keras'

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:
  'tm', 'plyr', 'reshape2', 'rgexf', 'httpuv'
checkRd: (-1) aminoAcidFun.Rd:37: Lost braces
    37 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the amino acids at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
checkRd: (-1) vlfFun.Rd:36: Lost braces
    36 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the nucleotides at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RTransferEntropy’

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: ‘OpenImageR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'VMDecomp', 'forecast', 'nnfor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'nnfor', 'VMDecomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'imager', 'pdftools'

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: ‘ddpcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'FSA', 'ggpubr', 'phia', 'plotly', 'soundgen', 'rcompanion',
  'shiny', 'shinyFiles', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BCEA', 'INLA', 'sf', 'heemod'
Package unavailable to check Rd xrefs: ‘INLA’
Packages required but not available: 'Rcpp', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'ggpubr', 'Rfast'

Packages suggested but not available for checking:
  'DESeq2', 'qvalue', 'easylabel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'shiny'

Package suggested but not available for checking: ‘safetyGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'diverse', 'geosphere'
Packages required but not available:
  'fields', 'ggtext', 'metR', 'modEvA', 'rangeBuilder', 'terra', 'sf'

Package suggested but not available for checking: ‘rnaturalearth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyjs', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
Packages required but not available: 'httpuv', 'shiny', 'tm', 'wordcloud'

Packages suggested but not available for checking:
  'DT', 'shinydashboard', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'httpuv', 'robotstxt', 'tidytext', 'urltools'
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spelling', 'vcr'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(votesmart)
  > 
  > abrams_id <- 67385
  > aoc_id <- 180416
  > pelosi_id <- 26732
  > obama_id <- 9490
  > pete_id <- 127151
  > warren_id <- 141272
  > 
  > test_check("votesmart")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/votesmart.Rcheck/tests/testthat/helper-vcr.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("votesmart")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/helper-vcr.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Packages required but not available: 'lmerTest', 'gamm4', 'oro.nifti'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'geometry', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'oce', 'interp', 'magick', 'metR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘MixGHD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survminer', 'flexsurv', 'ggpubr'

Package suggested but not available for checking: ‘plotly’

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: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'invertiforms', 'RSpectra'

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aquaporin.Rd:10: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) vsts_create_release.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:34: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'ranger', 'Rborist'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘bayesreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survey’
Packages required but not available: 'DiagrammeRsvg', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘plyr’

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: ‘findR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘polyglotr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'datamods', 'DescTools', 'DT', 'rintrojs', 'rstatix', 'shiny',
  'shinyjs', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpubr', 'shiny', 'shinycssloaders', 'shinydashboard',
  'shinydashboardPlus', 'shinyWidgets', 'plotly', 'DT'

Packages suggested but not available for checking: 'waiter', 'spsComps'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Found the following HTML validation problems:
get_logger.html:57:1 (get_logger.Rd:21): Warning: trimming empty <dt>
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACSreadAgroclim.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'tokenizers', 'text2vec'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geosphere', 'ggforce', 'lwgeom', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'rstan', 'Rcpp', 'rstantools', 'RcppArmadillo',
  'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘diagis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'leaflet', 'DT', 'ecospat', 'ENMeval', 'geodata',
  'knitcitations', 'leafem', 'leaflet.extras', 'sf', 'shinyalert',
  'shinyjs', 'shinyWidgets', 'spocc', 'spThin'

Packages suggested but not available for checking:
  'ade4', 'BIEN', 'dismo', 'mapview', 'maxnet', 'occCite',
  'rangeModelMetadata', 'raster', 'rgbif', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'prodlim', 'riskRegression'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WRS2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Running examples in ‘WALS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: controlGLM
> ### Title: Control function for initial GLM fit
> ### Aliases: controlGLM
> 
> ### ** Examples
> 
> data("HMDA", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readtext', 'flextable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'bioacoustics'

Packages suggested but not available for checking:
  'ape', 'soundgen', 'leaflet', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fda', 'fields', 'reshape2', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'SPEI', 'devtools'
Error(s) in re-building vignettes:
  ...
--- re-building ‘WASP.Rmd’ using rmarkdown

Quitting from lines 34-46 [packages] (WASP.Rmd)
Error: processing vignette 'WASP.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘WASP.Rmd’

SUMMARY: processing the following file failed:
  ‘WASP.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'caret'

Packages suggested but not available for checking:
  'tmap', 'tmaptools', 'sf'

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: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'caretForecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'caretForecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'caretForecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'caretForecast', 'TSLSTM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'WaveletML', 'CEEMDANML'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'tsutils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'forecast', 'tsutils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'DecomposeR', 'DescTools', 'colorednoise', 'reshape2', 'astrochron',
  'biwavelet', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'geosphere'

Package suggested but not available for checking: ‘lwgeom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kimisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘BalancedSampling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'prospectr', 'spectacles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'latticeExtra', 'bindrcpp'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown

Quitting from lines 36-51 [libraries] (examples.Rmd)
Error: processing vignette 'examples.Rmd' failed with diagnostics:
there is no package called 'latticeExtra'
--- failed re-building ‘examples.Rmd’

SUMMARY: processing the following file failed:
  ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'fields', 'sf', 'spdep'

Packages suggested but not available for checking:
  'applicable', 'caret', 'CAST', 'exactextractr', 'recipes',
  'spatialsample', 'terra', 'tidymodels', 'tigris', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spelling', 'lemon'
Error(s) in re-building vignettes:
  ...
--- re-building ‘wcde.Rmd’ using rmarkdown

Quitting from lines 277-289 [unnamed-chunk-23] (wcde.Rmd)
Error: processing vignette 'wcde.Rmd' failed with diagnostics:
there is no package called 'lemon'
--- failed re-building ‘wcde.Rmd’

SUMMARY: processing the following file failed:
  ‘wcde.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘datanugget’

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.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘caret’
Packages required but not available: 'minqa', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'binman', 'semver'

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:
  'CVXR', 'rARPACK', 'RcppXPtrUtils', 'wdm', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arcpullr', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'chromote', 'lwgeom'

Packages suggested but not available for checking: 'ggmap', 'prepr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'RHRV', 'padr', 'varian'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'crul', 'magick', 'sf', 'stars', 'terra'

Packages suggested but not available for checking: 'spelling', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'wordcloud', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'uaparserjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'robotstxt', 'vcr'
checkRd: (-1) get_cid.Rd:58-59: Lost braces
    58 | <structure search> is assembled as "{\code{substructure} |
       |                                     ^
checkRd: (-1) get_cid.Rd:59-60: Lost braces
    59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
       |                                                                ^
checkRd: (-1) get_cid.Rd:70-71: Lost braces
    70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
       |  ^
checkRd: (-1) get_cid.Rd:71-72: Lost braces
    71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
       |                                                      ^
Package required but not available: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httpuv', 'promises'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘servr’
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quarto’
Package suggested but not available for checking: ‘httpuv’
Packages required but not available: 'apcluster', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonio', 'httpuv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'urltools', 'crul'

Package suggested but not available for checking: ‘vcr’

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: ‘Rcpp’

Packages suggested but not available for checking:
  'iptools', 'urltools', 'rgeolocate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'flextable', 'rrtable', 'ztable', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GGally', 'bayesplot', 'brms', 'dismo', 'glmnet', 'jtools',
  'rstanarm', 'rstantools'

Packages suggested but not available for checking: 'reshape2', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'chromote', 'later', 'promises'

Packages suggested but not available for checking: 'httpuv', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'httpuv', 'shiny'
Package required but not available: ‘later’

Package suggested but not available for checking: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘adaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httpuv’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(webutils)
  > 
  > test_check("webutils")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 14 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-echo.R:14:3'): test echo from httpuv ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'httpuv'
  Backtrace:
      ▆
   1. ├─curl::curl_echo(h, port = httpuv::randomPort()) at test-echo.R:14:3
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-echo.R:55:3'): Echo a big file ─────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'httpuv'
  Backtrace:
      ▆
   1. ├─curl::curl_echo(h, port = httpuv::randomPort()) at test-echo.R:55:3
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 14 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'tidytext', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘WeibullR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'learnr', 'WeibullR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'WeibullR', 'plotly'

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:
  'WeibullR', 'WeibullR.plotly', 'shiny', 'shinydashboard'

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'pROC', 'glmnet', 'geometry'
checkRd: (-1) WeightedROC.Rd:10: Lost braces; missing escapes or markup?
    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
Running examples in ‘WeightedROC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: WeightedAUC
> ### Title: WeightedAUC
> ### Aliases: WeightedAUC
> 
> ### ** Examples
> 
> 
> library(WeightedROC)
> ## Compute the AUC for this weighted data set.
> y <- c(0, 0, 1, 1, 1)
> w <- c(1, 1, 1, 4, 5)
> y.hat <- c(1, 2, 3, 1, 1)
> tp.fp <- WeightedROC(y.hat, y, w)
> (wauc <- WeightedAUC(tp.fp))
[1] 0.325
> 
> ## For the un-weighted ROCR example data set, verify that our AUC is
> ## the same as that of ROCR/pROC.
> if(require(microbenchmark) && require(ROCR) && require(pROC)){
+   data(ROCR.simple, envir=environment())
+   microbenchmark(WeightedROC={
+     tp.fp <- with(ROCR.simple, WeightedROC(predictions, labels))
+     wroc <- WeightedAUC(tp.fp)
+   }, ROCR={
+     pred <- with(ROCR.simple, prediction(predictions, labels))
+     rocr <- performance(pred, "auc")@y.values[[1]]
+   }, pROC={
+     proc <- pROC::auc(labels ~ predictions, ROCR.simple, algorithm=2)
+   }, times=10)
+   rbind(WeightedROC=wroc, ROCR=rocr, pROC=proc) #same
+ }
Loading required package: microbenchmark
Loading required package: ROCR
Loading required package: pROC
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘pROC’
> 
> ## For the un-weighted pROC example data set, verify that our AUC is
> ## the same as that of ROCR/pROC.
> data(aSAH, envir=environment())
Warning in data(aSAH, envir = environment()) :
  data set ‘aSAH’ not found
> table(aSAH$s100b)
Error: object 'aSAH' not found
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("WeightedROC")
  Loading required package: WeightedROC
  label
  -1 
   4 
  label
  1 
  4 
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-auc.R:53:1'): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(geometry)`: there is no package called 'geometry'
  Backtrace:
      ▆
   1. └─base::library(geometry) at test-auc.R:53:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
checkRd: (-1) CLIC.Rd:149: Lost braces
   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'sf', 'RcppCGAL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'CBPS', 'optweight', 'logistf', 'osqp', 'marginaleffects'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
Packages required but not available: 'mice', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dbscan', 'interpolation', 'ks', 'stray'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'minqa'

Packages suggested but not available for checking: 'EdSurvey', 'glmmTMB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pROC', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'freealg', 'spray'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'emstreeR', 'terra', 'sf'

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: ‘SKAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'tokenizers', 'anytime', 'qdap', 'ggwordcloud', 'ggmap'

Package suggested but not available for checking: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DiagrammeRsvg', 'pander'
Error(s) in re-building vignettes:
  ...
--- re-building ‘when.Rmd’ using rmarkdown

Quitting from lines 322-324 [unnamed-chunk-22] (when.Rmd)
Error: processing vignette 'when.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘when.Rmd’

SUMMARY: processing the following file failed:
  ‘when.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'shiny', 'miniUI', 'anomalize', 'ggforce', 'ggtext'
Running ‘testthat.R’ [57s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(whippr)
  > 
  > test_check("whippr")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-incremental.R:67:3'): plot_incremental ramp works ──────────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `plot_incremental(ramp_normalized)`: The package "ggforce" is required.
  Backtrace:
      ▆
   1. ├─testthat::expect_s3_class(...) at test-incremental.R:67:3
   2. │ └─testthat::quasi_label(enquo(object), arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─whippr::plot_incremental(ramp_normalized)
   5. └─whippr:::plot_incremental.ramp(ramp_normalized)
   6.   └─rlang::check_installed("ggforce")
  ── Error ('test-incremental.R:93:3'): plot_incremental step works ──────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ggforce'
  Backtrace:
      ▆
   1. ├─testthat::expect_s3_class(...) at test-incremental.R:93:3
   2. │ └─testthat::quasi_label(enquo(object), arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─whippr::plot_incremental(ramp_normalized)
   5. ├─whippr:::plot_incremental.step(ramp_normalized)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base (local) withOneRestart(expr, restarts[[1L]])
   9.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'terra', 'sf', 'raster'
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'oro.nifti', 'neurobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘ggfx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggraph', 'plyr', 'srvyr', 'TAM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'reshape2', 'tidytext'

Packages suggested but not available for checking: 'fuzzyjoin', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_geo_box.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘units’

Package suggested but not available for checking: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'move2', 'adehabitatLT', 'sf', 'units', 'lwgeom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'plotly', 'shinydashboard', 'DT', 'colourpicker', 'shinyjs',
  'plyr', 'reshape', 'rintrojs', 'ggrepel', 'DESeq2', 'FactoMineR',
  'factoextra', 'heatmaply', 'shinycssloaders', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'phytools', 'geiger', 'ape', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rnrfa’
Packages required but not available:
  'automap', 'gdistance', 'hierfstat', 'pegas', 'raster', 'sf',
  'terra', 'vcfR'

Packages suggested but not available for checking:
  'adegenet', 'devtools', 'SpatialKDE'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ks', 'plm', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen',
  'StanHeaders'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggpubr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'secr', 'shiny'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘sf’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cvCovEst', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘lamW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dtwclust', 'Rcpp'

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 checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘pander’
Error(s) in re-building vignettes:
  ...
--- re-building ‘woodsimulatr_basics.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (woodsimulatr_basics.Rmd)
Error: processing vignette 'woodsimulatr_basics.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘woodsimulatr_basics.Rmd’

SUMMARY: processing the following file failed:
  ‘woodsimulatr_basics.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Found the following HTML validation problems:
benefits.html:96:1 (benefits.Rd:39): Warning: trimming empty <h3>
beveridge.html:66:1 (beveridge.Rd:29): Warning: trimming empty <h3>
happiness.html:141:1 (happiness.Rd:54): Warning: trimming empty <h3>
hprice3.html:99:1 (hprice3.Rd:40): Warning: trimming empty <h3>
Package required but not available: ‘ranger’

Packages suggested but not available for checking: 'tidySEM', 'missRanger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘shiny’
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quanteda', 'ggrepel'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘wordnetDicts’
Package required but not available: ‘LambertW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) wordpiece_cache_dir.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'text2vec', 'word2vec', 'fastTextR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httpuv’

Packages suggested but not available for checking:
  'miniUI', 'reticulate', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tune’

Packages suggested but not available for checking:
  'finetune', 'recipes', 'spelling', 'tidyclust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘recipes’
Running examples in ‘workflows-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_recipe
> ### Title: Add a recipe to a workflow
> ### Aliases: add_recipe remove_recipe update_recipe
> 
> ### ** Examples
> 
> library(recipes)
Error in library(recipes) : there is no package called ‘recipes’
Execution halted
Package suggested but not available for checking: ‘fuzzyjoin’
Packages required but not available: 'rnaturalearth', 'sf', 'ggfx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openair', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dtwclust', 'clusterSim', 'aricode', 'Rtsne', 'uwot', 'factoextra',
  'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggtext', 'ggfittext'

Package suggested but not available for checking: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GGally’

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:
  'reshape2', 'ggrepel', 'DT', 'tidytext', 'ggraph', 'ggwordcloud'

Packages suggested but not available for checking: 'fst', 'flexdashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'shinythemes', 'shinyjs', 'plyr', 'reshape2', 'DT'

Package suggested but not available for checking: ‘wpp2015’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'oem', 'Rcpp', 'rqPen', 'RcppEigen', 'RcppCGAL', 'RSpectra'

Packages suggested but not available for checking: 'transport', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MBC’

Package suggested but not available for checking: ‘wmtsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gWQS', 'extraDistr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DescTools', 'flextable'

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'factoextra', 'FactoMineR'
Error(s) in re-building vignettes:
  ...
--- re-building ‘wrGraphVignette1.Rmd’ using rmarkdown

Quitting from lines 27-33 [setup] (wrGraphVignette1.Rmd)
Error: processing vignette 'wrGraphVignette1.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘wrGraphVignette1.Rmd’

SUMMARY: processing the following file failed:
  ‘wrGraphVignette1.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'fdapace', 'fdadensity', 'Rfast', 'CVXR', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘spelling’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [24s/32s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages suggested but not available for checking: 'qvalue', 'Rcpp'
Package suggested but not available for checking: ‘ROTS’
Package required but not available: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape', 'plyr'

Packages suggested but not available for checking:
  'car', 'mediation', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'kimisc', 'knitcitations', 'metap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'fields', 'forecast'

Packages suggested but not available for checking: 'EGRET', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'PL94171', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘tidycensus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘latticeExtra’

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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
Packages required but not available: 'plyr', 'reshape2', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Packages required but not available: 'Rcpp', 'simts', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sde', 'ftsa', 'rainbow', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Packages suggested but not available for checking:
  'reshape2', 'ggpubr', 'padr', 'SpecsVerification'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) exploreSignatures.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
checkRd: (-1) qualifyFunctionArguments.Rd:14: Lost braces
    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
Package required but not available: ‘imager’

Package suggested but not available for checking: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘xaringan’
Running examples in ‘xaringanExtra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: logo
> ### Title: Add Logo
> ### Aliases: logo use_logo html_dependency_logo
> 
> ### ** Examples
> 
> xaringan_logo <- file.path(
+   "https://raw.githubusercontent.com/rstudio/hex-stickers/master",
+   "PNG/xaringan.png"
+ )
> use_logo(xaringan_logo)
Error in utils::packageVersion("xaringan") : 
  there is no package called ‘xaringan’
Calls: use_logo ... html_dependency_logo -> %||% -> xaringan_version -> <Anonymous>
Execution halted
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xaringanExtra)
  > 
  > test_check("xaringanExtra")
  [ FAIL 3 | WARN 0 | SKIP 8 | PASS 150 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-banner.R:28:5', 'test-banner.R:43:5',
    'test-banner.R:77:5', 'test-freezeframe.R:35:5', 'test-panelset.R:2:3',
    'test-scribble.R:35:5', 'test-search.R:31:5', 'test-search.R:46:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-panelset.R:113:3'): panelset knitr chunks with plots ───────────
  <callr_status_error/callr_error/rlib_error_3_0/rlib_error/error/condition>
  Error: ! in callr subprocess.
  Caused by error in `loadNamespace(x)`:
  ! there is no package called ‘xaringan’
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-panelset.R:113:3
   2.   └─rlang::cnd_signal(state$error)
  ── Error ('test-panelset.R:132:3'): panelset knitr chunks with custom tab names ──
  <callr_status_error/callr_error/rlib_error_3_0/rlib_error/error/condition>
  Error: ! in callr subprocess.
  Caused by error in `loadNamespace(x)`:
  ! there is no package called ‘xaringan’
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-panelset.R:132:3
   2.   └─rlang::cnd_signal(state$error)
  ── Error ('test-panelset.R:151:3'): panelset knitr chunks with mutiple outputs ──
  <callr_status_error/callr_error/rlib_error_3_0/rlib_error/error/condition>
  Error: ! in callr subprocess.
  Caused by error in `loadNamespace(x)`:
  ! there is no package called ‘xaringan’
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-panelset.R:151:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 3 | WARN 0 | SKIP 8 | PASS 150 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘servr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘xaringan’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggdist’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rugarch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) xshow.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) xshow.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chemnet.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chemnet.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:105: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘bupaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'magick', 'qs'
Running examples in ‘xfun-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: shrink_images
> ### Title: Shrink images to a maximum width
> ### Aliases: shrink_images
> 
> ### ** Examples
> 
> f = xfun:::all_files("[.](png|jpe?g)$", R.home("doc"))
> file.copy(f, tempdir())
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> f = file.path(tempdir(), basename(f))
> magick::image_info(magick::image_read(f))  # some widths are larger than 300
Error in loadNamespace(x) : there is no package called ‘magick’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
Package suggested but not available for checking: ‘Ckmeans.1d.dp’
GNU make is a SystemRequirements.
Running examples in ‘xgboost-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xgb.ggplot.importance
> ### Title: Plot feature importance as a bar graph
> ### Aliases: xgb.ggplot.importance xgb.plot.importance
> 
> ### ** Examples
> 
> data(agaricus.train)
> ## Keep the number of threads to 2 for examples
> nthread <- 2
> data.table::setDTthreads(nthread)
> 
> bst <- xgboost(
+   data = agaricus.train$data, label = agaricus.train$label, max_depth = 3,
+   eta = 1, nthread = nthread, nrounds = 2, objective = "binary:logistic"
+ )
[1]	train-logloss:0.161178 
[2]	train-logloss:0.064728 
> 
> importance_matrix <- xgb.importance(colnames(agaricus.train$data), model = bst)
> 
> xgb.plot.importance(importance_matrix, rel_to_first = TRUE, xlab = "Relative importance")
> 
> (gg <- xgb.ggplot.importance(importance_matrix, measure = "Frequency", rel_to_first = TRUE))
Error: Ckmeans.1d.dp package is required
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DescTools', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mexhaz’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'glmnet', 'mixOmics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mpoly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'qpdf', 'pdftools'
Package required but not available: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
'LazyData' is specified without a 'data' directory
Running examples in ‘xplain-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xplain
> ### Title: Showing interpretation information for the results of a function
> ### Aliases: xplain
> 
> ### ** Examples
> 
> 
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Packages required but not available: 'Rcpp', 'shiny'

Packages suggested but not available for checking:
  'blorr', 'DT', 'olsrr', 'plotly', 'rfm', 'shinyBS',
  'shinycssloaders', 'standby'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FactoMineR', 'tm', 'ggforce', 'ggrepel', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Error(s) in re-building vignettes:
  ...
--- re-building ‘agency_standards.Rmd’ using rmarkdown
--- finished re-building ‘agency_standards.Rmd’

--- re-building ‘deepdive.Rmd’ using rmarkdown

Quitting from lines 14-22 [unnamed-chunk-1] (deepdive.Rmd)
Error: processing vignette 'deepdive.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘deepdive.Rmd’

--- re-building ‘xportr.Rmd’ using rmarkdown

Quitting from lines 14-22 [unnamed-chunk-1] (xportr.Rmd)
Error: processing vignette 'xportr.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘xportr.Rmd’

SUMMARY: processing the following files failed:
  ‘deepdive.Rmd’ ‘xportr.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'xpose', 'nlmixr2est'

Package suggested but not available for checking: ‘nlmixr2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggforce’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'fuzzyjoin'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'bigmemory', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plm’
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Packages required but not available: 'plm', 'sampleSelection'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'selectiveInference', 'lbfgs'

Package suggested but not available for checking: ‘pROC’

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.
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSpectra’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ccaPP’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘units’

Package suggested but not available for checking: ‘tablet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘probably’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘BayesFactor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

Package suggested but not available for checking: ‘spelling’

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', 'RcppArmadillo'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘MBESS’
checkRd: (-1) boot.yhat.Rd:3: Lost braces
     3 | \title{Bootstrap metrics produced from /code{calc.yhat}}
       |                                             ^
checkRd: (-1) boot.yhat.Rd:19: Lost braces
    19 |     Ouput of /code{lm}
       |                   ^
checkRd: (-1) boot.yhat.Rd:22: Lost braces
    22 |     Output of /code{calc.yhat}
       |                    ^
checkRd: (-1) booteval.yhat.rd:3: Lost braces
     3 | \title{Evaluate bootstrap metrics produced from /code{calc.yhat}}
       |                                                      ^
checkRd: (-1) booteval.yhat.rd:5: Lost braces
     5 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) combCI.rd:26: Lost braces
    26 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) commonality.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) dombin.rd:12: Lost braces
    12 |     Output from /code{dominance}
       |                      ^
checkRd: (-1) dominance.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) plotCI.yhat.rd:5: Lost braces
     5 |   This function plots CIs that have been produced from /code{booteval.yhat}.
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:32: Lost braces
    32 |   This function plots CIs that have been produced from /code{booteval.yhat}.   
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:35: Lost braces
    35 | This returns a plot of CIs that have been produced from /code{booteval.yhat}.
       |                                                              ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'blogdown', 'miniUI', 'shiny', 'shinyBS', 'spelling', 'xaringan'
Running examples in ‘ymlthis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: yml_params
> ### Title: Parameterize an R Markdown report using Shiny components
> ### Aliases: yml_params shiny_params shiny_checkbox shiny_numeric
> ###   shiny_slider shiny_date shiny_text shiny_file shiny_radio
> ###   shiny_select shiny_password
> 
> ### ** Examples
> 
> 
> yml() %>%
+   yml_params(
+     z = "z",
+     x = shiny_numeric("Starting value", 23),
+     no = shiny_checkbox("No option?"),
+     y = shiny_slider("Data range", 0, 1, .5, round = TRUE)
+   )
Error in stop_if_not_installed("shiny") : 
  The package "shiny" is required Must be installed to use this function.
Calls: %>% ... stop_if_shiny_not_installed -> stop_if_not_installed -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-ymlthis.Rmd’ using rmarkdown

Quitting from lines 126-133 [unnamed-chunk-8] (introduction-to-ymlthis.Rmd)
Error: processing vignette 'introduction-to-ymlthis.Rmd' failed with diagnostics:
The package "shiny" is required Must be installed to use this function.
--- failed re-building ‘introduction-to-ymlthis.Rmd’

--- re-building ‘yaml-fieldguide.Rmd’ using rmarkdown
--- finished re-building ‘yaml-fieldguide.Rmd’

--- re-building ‘yaml-overview.Rmd’ using rmarkdown
--- finished re-building ‘yaml-overview.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-ymlthis.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spelling', 'eulerr', 'Peptides'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DT', 'shinyjs', 'shiny', 'shinydashboard', 'shinyBS', 'yuima',
  'sde', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cubature', 'Rcpp', 'calculus', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RNRCS', 'metScanR', 'rnoaa'
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'tidycensus', 'mapview'
Error(s) in re-building vignettes:
  ...
--- re-building ‘a01_introduction.Rmd’ using rmarkdown
--- finished re-building ‘a01_introduction.Rmd’

--- re-building ‘a02_workflow-tidycensus.Rmd’ using rmarkdown

Quitting from lines 18-21 [setup] (a02_workflow-tidycensus.Rmd)
Error: processing vignette 'a02_workflow-tidycensus.Rmd' failed with diagnostics:
there is no package called 'tidycensus'
--- failed re-building ‘a02_workflow-tidycensus.Rmd’

--- re-building ‘a03_developer-notes.Rmd’ using rmarkdown
--- finished re-building ‘a03_developer-notes.Rmd’

SUMMARY: processing the following file failed:
  ‘a02_workflow-tidycensus.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'Rcpp'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lomb’

Package suggested but not available for checking: ‘xsp’

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.
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking: 'qrmtools', 'rugarch'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘polite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rtsne', 'reshape2', 'mixtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SKAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘estimatr’
Package suggested but not available for checking: ‘lme4’
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(ZIBR)
  Loading required package: statmod
  > 
  > test_check("ZIBR")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-simulations.R:51:3'): simulate_logistic_data works ─────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-simulations.R:51:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DT', 'spelling'
Package suggested but not available for checking: ‘devtools’
checkRd: (-1) label_kansuji.Rd:48: Lost braces; missing escapes or markup?
    48 | but if TRUE and installed '{scales}` package, 1.10 will be displayed.}
       |                            ^
Found the following HTML validation problems:
kana.html:65:1 (kana.Rd:33): Warning: trimming empty <dt>
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'tidycensus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘trustOptim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tolerance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'tidycensus', 'tigris'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using knitr

Quitting from lines 44-51 [unnamed-chunk-2] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'ggrepel'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘webmockr’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(zoltr)
  > 
  > test_check("zoltr")
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-connection.R:8:1'): (code run outside of `test_that()`) ────────
  <packageNotFoundError/error/condition>
  Error in `library(webmockr)`: there is no package called 'webmockr'
  Backtrace:
      ▆
   1. └─base::library(webmockr) at test-connection.R:8:1
  ── Error ('test-job.R:28:3'): job_data() column types are correct for forecast CSV data ──
  Error in `to_return(., status = 200, headers = list(`Content-Type` = "text/csv"))`: could not find function "to_return"
  Backtrace:
      ▆
   1. └─... %>% ...
  ── Error ('test-job.R:52:3'): job_data() column types are correct for truth CSV data ──
  Error in `to_return(., status = 200, headers = list(`Content-Type` = "text/csv"))`: could not find function "to_return"
  Backtrace:
      ▆
   1. └─... %>% ...
  ── Error ('test-model.R:7:1'): (code run outside of `test_that()`) ─────────────
  <packageNotFoundError/error/condition>
  Error in `library(webmockr)`: there is no package called 'webmockr'
  Backtrace:
      ▆
   1. └─base::library(webmockr) at test-model.R:7:1
  ── Error ('test-project.R:6:1'): (code run outside of `test_that()`) ───────────
  <packageNotFoundError/error/condition>
  Error in `library(webmockr)`: there is no package called 'webmockr'
  Backtrace:
      ▆
   1. └─base::library(webmockr) at test-project.R:6:1
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'tmap', 'tmaptools', 'pct', 'lwgeom', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlearning', 'shiny', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘collapse’

Package suggested but not available for checking: ‘fuzzyjoin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magick', 'openxlsx', 'paws'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) in.zoom.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:13: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘AER’
Note: skipping ‘zoo.Rnw’ due to unavailable dependencies: 'AER'
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘shinythemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'mixtools', 'RcppEigen', 'RcppNumerical'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'glmnet', 'Rlinsolve', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  29.2Mb
checkRd: (-1) abclass.Rd:133: Lost braces; missing escapes or markup?
   133 |     \code{abclass.control()} returns an object of class {abclass.control}
       |                                                         ^
checkRd: (-1) supclass.Rd:109: Lost braces; missing escapes or markup?
   109 | to solve the equivalent linear programming problem via the package {Rglpk}.
       |                                                                    ^
checkRd: (-1) supclass.Rd:110: Lost braces; missing escapes or markup?
   110 | It is recommended to use a recent version of {GLPK}.
       |                                              ^
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is 105.5Mb
  sub-directories of 1Mb or more:
    libs  104.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_ex_data.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:30: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   2.9Mb
    libs      8.1Mb
Running ‘testthat.R’ [332s/361s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9. │     │ └─base::withCallingHandlers(...)
   10. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   11. └─abn::buildScoreCache(...)
   12.   └─abn::buildScoreCache.bayes(...)
   13.     └─... %do% ...
   14.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
   15.         └─base::library(p, character.only = TRUE)
  
  [ FAIL 7 | WARN 0 | SKIP 56 | PASS 444 ]
  Deleting unused snapshots:
  • tographviz/graph.dot
  • tographviz/graph1.dot
  • tographviz/graph_group.dot
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
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    include  13.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) bind_tweets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bind_tweets.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) accelimp.Rd:15: Lost braces
    15 | \item[]{...}
       |        ^
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Specified C++11: please drop specification unless essential
checkRd: (-1) overstallwoods.Rd:184-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:186-187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:188-189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:190-191: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 11.7Mb
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    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
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    doc    1.7Mb
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    R  14.6Mb
checkRd: (-1) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) est_S_Plus_Plus_MethodA.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Plus_Plus_MethodB.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method B}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodA.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
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    29 |   \item{trt_diff}{Estimate of treatment difference for S_{*+} using Method B}
       |                                                          ^
Specified C++11: please drop specification unless essential
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    25 |   \item{gatype}{Type of GA. \itemize{\item{"gga": generational GA}  \item{"ssga": steady state GA} } {Default value is "gga"}}
       |                                                                                                      ^
checkRd: (-1) adana.Rd:26: Lost braces; missing escapes or markup?
    26 |   \item{objective}{Type of optimization. \itemize{\item{"min": minimization}  \item{"max": maximization} } {Default value is "max"}}
       |                                                                                                            ^
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    34 |                  {Default value is "initbin"}}
       |                  ^
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    56 |                \itemize{\item{"integer"}  \item{"real"} } {Default value is "real"}}
       |                                                           ^
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   185 |     {Default value is "w"}
       |     ^
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checkRd: (-1) adapt.Rd:46: Lost braces
    46 | \item{qvals}{a vector of values in [0, 1]U{Inf}. Q-values. See Details}
       |                                           ^
checkRd: (-1) corr_lfdr.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) corr_lfdr.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
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    40 | \code{plot_2d_lfdr} gives the contour plot of local FDR estimates when all p-values are equal to \code{targetp}. It is recommended to run \code{plot_2d_lfdr} for multiple \code{targetp}'s ranging from {0.001, 0.005, 0.01, 0.05}.
       |                                                                                                                                                                                                          ^
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
installed size is  7.5Mb
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    doc   7.1Mb
checkRd: (-1) SVMDECON.Rd:23: Lost braces; missing escapes or markup?
    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
installed size is  5.7Mb
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installed size is 13.5Mb
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    libs  13.4Mb
'LazyData' is specified without a 'data' directory
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installed size is  9.1Mb
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    R      2.0Mb
    data   3.0Mb
    libs   2.5Mb
checkRd: (-1) varipart.Rd:19: Lost braces
    19 | \item{type}{a character specifying the algorithm which should be used to adjust R-squared (either \code{"simulated"} or \ code{"parametric"}).}
       |                                                                                                                               ^
installed size is  5.3Mb
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    R     2.0Mb
    doc   2.7Mb
installed size is 151.9Mb
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    adelie    1.2Mb
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installed size is 10.4Mb
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    data  10.2Mb
installed size is  5.1Mb
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    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
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    doc   3.7Mb
checkRd: (-1) med.groups.Rd:20: Lost braces; missing escapes or markup?
    20 | medication groups using the construction \emph{"{NAME}"}.
       |                                                 ^
checkRd: (-1) med.groups.Rd:26: Lost braces; missing escapes or markup?
    26 | Another example is "NotVita" defined as "(!{Vitamines})", which selects all
       |                                            ^
installed size is  6.3Mb
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    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Amatdual.Rd:15: Lost braces
    15 |   \item{removelist}{a vector of indices into env{X} of the lifted coefficients during the transform (in the order of removal). }
       |                                                 ^
checkRd: (-1) fwtnp.Rd:30: Lost braces
    30 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lintr’ ‘pharmaversesdtm’ ‘pkgdown’ ‘testthat’
A package should be listed in only one of these fields.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
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checkRd: (-1) count_cases.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) count_cases.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) enrich.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) enrich.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) enrich.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) fitaep.Rd:14: Lost braces
    14 | \item A sequence of goodness-of-fit measures consist of Akaike Information Criterion (\code{AIC}), Consistent Akaike Information Criterion (\code{CAIC}), Bayesian Information Criterion (\code{BIC}), Hannan-Quinn information criterion (\code{HQIC}), Anderson-Darling (\code{AD}), Cram\'{e}er-von Misses (\code{CVM}), Kolmogorov-Smirnov (\code{KS}), and log-likelihood (\code{log-likelihood}) statistics.
       |                                                                                                                                                                                                                                                                                              ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) estimate.affinity.matrix.Rd:31: Lost braces; missing escapes or markup?
    31 | than \code{Y}, then those variables that appear in \code{X} but no in {Y}
       |                                                                       ^
checkRd: (-1) estimate.affinity.matrix.lowrank.Rd:36: Lost braces; missing escapes or markup?
    36 | \code{Y}, then those variables that appear in \code{X} but no in {Y} should
       |                                                                  ^
checkRd: (-1) show.correlations.Rd:47: Lost braces
    47 | code{ndims} dimensions. Defaults to all dimensions unless the latter are
       |     ^
'LazyData' is specified without a 'data' directory
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checkRd: (-1) getNetworkGridLayout.Rd:6-11: Lost braces
     6 | getCoordinatesFromVertexId2<-function(AFMImage, vId) {
       |                                                      ^
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    extdata   3.4Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Specified C++11: please drop specification unless essential
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) AEHMLE.Rd:42-45: Lost braces
    42 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) AHMLE.Rd:41-43: Lost braces
    41 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
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checkRd: (-1) CalOptimalDecision.Rd:45: Lost braces; missing escapes or markup?
    45 | A \code{data.frame} of (1) the probability that the optimal decision for each observation being d in {0,1,...,k}, (2) expected utility of binary version of judge's decision (g_d), (3) expected utility of binary DMF recommendation, and (4) the difference between (2) and (3). If \code{include.utility.diff.mcmc = TRUE}, returns a list of such \code{data.frame} and a \code{data.frame} that includes the result for mean and quantile of \code{Utility.diff.control.mcmc} and \code{Utility.diff.treated.mcmc} across mcmc samples.
       |                                                                                                      ^
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    39 |  \item \code{Variable} {1st column: The various aims to be completed}
       |                        ^
checkRd: (-1) aimPlot.Rd:40: Lost braces; missing escapes or markup?
    40 |  \item \code{Percentage} {2nd column: The percentage of completeness}
       |                          ^
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    65 | \emph{InputsPert}{[list] object of class \emph{InputsModel} containing the ensembles of perturbed model inputs required to perform data assimilation:}
       |                  ^
installed size is  8.0Mb
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    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
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    33 |   \item{las}{ Numeric in {0,1,2,3}; the style of axis labels. 
       |                          ^
checkRd: (-1) interpp.Rd:119: Lost braces
   119 |   If \code{linear} is \\code{TRUE}, linear
       |                             ^
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    61 |                                      names with the format {"Inferred1", "Inferred2", ...}.
       |                                                            ^
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checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
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checkRd: (-1) allestimates.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:26: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) compare_cohorts.Rd:35: Lost braces in \itemize; meant \describe ?
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
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Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test-update.R:111:5'): render_docs also transform new/modified vignettes if specified: docsify ──
  Error in `cat(out[[2]])`: argument 1 (type 'list') cannot be handled by 'cat'
  Backtrace:
      ▆
   1. └─altdoc::render_docs(path = getwd()) at test-update.R:111:5
   2.   └─altdoc:::.import_vignettes(...)
   3.     └─base::vapply(...)
   4.       └─altdoc (local) FUN(X[[i]], ...)
   5.         └─altdoc:::.render_one_vignette(...)
   6.           └─altdoc:::.qmd2md(origin, tar_dir, verbose = verbose, preamble = pre)
   7.             └─base::cat(out[[2]])
  
  [ FAIL 8 | WARN 0 | SKIP 8 | PASS 55 ]
  Error: Test failures
  Execution halted
checkRd: (-1) altopt.ic.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) altopt.rc.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
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Package suggested but not available for checking: ‘metaboliteIDmapping’
checkRd: (-1) convertCoord.Rd:32: Lost braces
    32 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) convertCoord.individual.Rd:33: Lost braces
    33 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.Rd:39: Lost braces
    39 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.individual.Rd:39: Lost braces
    39 | here{https://lbs.amap.com/faq/account/key/72}}
       |     ^
checkRd: (-1) getLocation.Rd:60: Lost braces; missing escapes or markup?
    60 | {https://lbs.amap.com/faq/account/key/72}}
       | ^
checkRd: (-1) getLocation.individual.Rd:60: Lost braces
    60 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
Specified C++11: please drop specification unless essential
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installed size is  5.7Mb
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Specified C++11: please drop specification unless essential
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory