Package required but not available: ‘qcr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BIFIEsurvey', 'progress', 'Hmisc', 'mice', 'car', 'reshape2',
  'miceadds', 'tidyr', 'EffectLiteR', 'eatGADS', 'janitor', 'lme4'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'R2jags', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ebayesthresh.Rmd’ using rmarkdown

Quitting from lines 25-28 [unnamed-chunk-2] (ebayesthresh.Rmd)
Error: processing vignette 'ebayesthresh.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘ebayesthresh.Rmd’

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'ncmeta', 'reshape2', 'stringr', 'tidyterra'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'ggplot2', 'ggridges', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dendextend', 'dplyr', 'ggplot2', 'purrr', 'stringr', 'tibble',
  'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Packages suggested but not available for checking:
  'dplyr', 'lubridate', 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ecb_sdw.Rmd’ using rmarkdown

Quitting from lines 29-31 [unnamed-chunk-1] (ecb_sdw.Rmd)
Error: processing vignette 'ecb_sdw.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘ecb_sdw.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Ecfun’

Package suggested but not available for checking: ‘systemfit’

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

Packages suggested but not available for checking:
  'car', 'DescTools', 'Ecdat', 'pryr', 'ipumsr', 'lubridate',
  'bayesplot', 'bssm', 'ggplot2', 'tibble', 'kableExtra', 'purrr',
  'EnvStats', 'drc', 'readxl'

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

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

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘echo-vignette.Rmd’ using rmarkdown

Quitting from lines 51-100 [unnamed-chunk-2] (echo-vignette.Rmd)
Error: processing vignette 'echo-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘echo-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘echo-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'stringr', 'purrr', 'tibble', 'tidyselect',
  'tidyr', 'forcats'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'progress', 'purrr', 'readr', 'tibble', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'geouy', 'haven', 'janitor', 'labelled', 'srvyr', 'statar',
  'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'furrr', 'ggplot2', 'patchwork', 'progress'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("ecmwfr")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'ggplot2', 'ggpubr'

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

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

Packages suggested but not available for checking: 'rvest', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'EML', 'ggplot2', 'lubridate', 'neonUtilities', 'stringr',
  'tidyr'

Packages suggested but not available for checking:
  'ritis', 'taxize', 'testthat', 'worrms', 'ggrepel'

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

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'ggplot2', 'ggraph', 'tidygraph'

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'dplyr', 'ggplot2', 'reshape2', 'tibble', 'cowplot'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘alphahull’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
checkRd: (-1) ecolRxC.Rd:161-166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:167-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:176-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:179-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:186-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:193-201: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:202-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:209-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:217-221: Lost braces in \itemize; meant \describe ?
Running examples in ‘ecolRxC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.ecolRxC
> ### Title: Graphical representation of a RxC ecological inference (vote
> ###   transfer) matrix
> ### Aliases: plot.ecolRxC
> 
> ### ** Examples
> 
> votes1 <- structure(list(P1 = c(16L, 4L, 13L, 6L, 1L, 16L, 6L, 17L, 48L, 14L),
+                          P2 = c(8L, 3L, 0L, 5L, 1L, 4L, 7L, 6L, 28L, 8L),
+                          P3 = c(38L, 11L, 11L, 3L, 13L, 39L, 14L, 34L, 280L, 84L),
+                          P4 = c(66L, 5L, 18L, 39L, 30L, 57L, 35L, 65L, 180L, 78L),
+                          P5 = c(14L, 0L, 5L, 2L, 4L, 21L, 6L, 11L, 54L, 9L),
+                          P6 = c(8L, 2L, 5L, 3L, 0L, 7L, 7L, 11L, 45L, 17L),
+                          P7 = c(7L, 3L, 5L, 2L, 3L, 17L, 7L, 13L, 40L, 8L)),
+                          row.names = c(NA, 10L), class = "data.frame")
> votes2 <- structure(list(C1 = c(2L, 1L, 2L, 2L, 0L, 4L, 0L, 4L, 19L, 14L),
+                          C2 = c(7L, 3L, 1L, 7L, 2L, 5L, 3L, 10L, 21L, 6L),
+                          C3 = c(78L, 7L, 28L, 42L, 28L, 84L, 49L, 85L, 260L, 100L),
+                          C4 = c(56L, 14L, 20L, 7L, 19L, 54L, 22L, 50L, 330L, 91L),
+                          C5 = c(14L, 3L, 6L, 2L, 3L, 14L, 8L, 8L, 45L, 7L)),
+                          row.names = c(NA, 10L), class = "data.frame")
> example <- ecolRxC(votes1, votes2, method = "IPF")
> p <- plot(example, show.plot = FALSE)
Error: Package ggplot2 needed for this function to work. Please install it.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'igraph', 'ggplot2'

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'biomod2', 'ecodist', 'Hmisc'

Packages suggested but not available for checking:
  'alphahull', 'dplyr', 'rms'

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

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

Packages suggested but not available for checking:
  'car', 'DHARMa', 'dplyr', 'GGally', 'ggplot2', 'ggthemes', 'gllvm',
  'glmmTMB', 'lme4', 'phylobase', 'phylosignal', 'reshape2', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'Hmisc', 'readr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RSQLite', 'dbplyr', 'dplyr', 'httr2', 'purrr', 'readr', 'readxl',
  'rvest', 'stringr', 'tibble', 'tidyr', 'tidyselect'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'smacof', 'ggplot2', 'hrbrthemes', 'reshape2', 'tidyr', 'viridis',
  'testthat'
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘JOPS’

Packages suggested but not available for checking:
  'ggplot2', 'ggraph', 'igraph', 'ggpubr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'smoof', 'reshape2', 'ggplot2', 'viridis', 'dplyr', 'plotly',
  'kableExtra'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘forecast’

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

Package suggested but not available for checking: ‘testthat’

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

Quitting from lines 54-55 [unnamed-chunk-4] (eCV_vignette.Rmd)
Error: processing vignette 'eCV_vignette.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘eCV_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'car', 'dae', 'dplyr', 'ggplot2', 'lmerTest', 'predictmeans',
  'supernova'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'haven', 'labelled', 'purrr', 'readr',
  'stringr', 'tibble', 'tidyr', 'tidyselect'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eddington.Rmd’ using rmarkdown

Quitting from lines 16-26 [unnamed-chunk-1] (eddington.Rmd)
Error: processing vignette 'eddington.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘eddington.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'bupaR', 'dplyr', 'ggplot2', 'ggthemes', 'tibble', 'tidyr',
  'lubridate', 'purrr', 'stringr', 'hms'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) read.edf.Rd:30: Lost braces
    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
Packages suggested but not available for checking: 'testthat', 'ggplot2'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'purrr', 'httptest', 'devtools', 'dplyr', 'tidyr',
  'roxygen2', 'pkgdown'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(httptest)
  Error in library(httptest) : there is no package called 'httptest'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘edgarWebR.Rmd’ using rmarkdown

Quitting from lines 17-26 [setup] (edgarWebR.Rmd)
Error: processing vignette 'edgarWebR.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘edgarWebR.Rmd’

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

Quitting from lines 16-22 [setup] (parsing.Rmd)
Error: processing vignette 'parsing.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘parsing.Rmd’

SUMMARY: processing the following files failed:
  ‘edgarWebR.Rmd’ ‘parsing.Rmd’

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

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

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

Package suggested but not available for checking: ‘huge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'vctrs', 'tibble', 'pillar', 'tidyselect', 'nestr', 'dae', 'dplyr'

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

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

Package suggested but not available for checking: ‘testthat’

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

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

Packages suggested but not available for checking:
  'testthat', 'dtplyr', 'vctrs', 'RSQLite', 'dbplyr', 'dm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'OCNet', 'rivnet', 'BayesianTools', 'DHARMa'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'readr', 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) items_ordered_eclsk_atl.Rd:23: Lost braces; missing escapes or markup?
    23 | \item \code{P4SRS10}: Keep working at something until {he/she} is finished?
       |                                                       ^
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'ggplot2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'Dire', 'haven', 'lme4', 'readxl', 'tibble', 'WeMix'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'rstanarm', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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.
Packages required but not available:
  'keras', 'tensorflow', 'tsutils', 'TSdeeplearning'

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: 'reshape2', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'
Running ‘test_checks.R’ [0s/1s]
  Running ‘test_donothing.R’ [0s/1s]
  Running ‘test_estim.R’ [1s/2s]
  Comparing ‘test_estim.Rout’ to ‘test_estim.Rout.save’ ... OK
  Running ‘test_factor.R’ [0s/1s]
  Running ‘test_factors.R’ [1s/2s]
  Running ‘test_prior_ff.R’ [1s/2s]
  Running ‘test_split.R’ [0s/1s]
  Running ‘test_transprobs.R’ [0s/1s]
Running the tests in ‘tests/test_checks.R’ failed.
Complete output:
  > library(efdm)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/test_donothing.R’ failed.
Complete output:
  > library(efdm)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/test_factor.R’ failed.
Complete output:
  > library(efdm)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/test_split.R’ failed.
Complete output:
  > data.table::setDTthreads(1)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/test_transprobs.R’ failed.
Complete output:
  > library(efdm)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown

Quitting from lines 47-50 [setup] (example.Rmd)
Error: processing vignette 'example.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘example.Rmd’

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

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

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

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

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

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

Packages suggested but not available for checking:
  'testthat', 'lavaan.survey'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'see', 'afex', 'BayesFactor', 'brms', 'car', 'gt', 'lme4',
  'lmerTest', 'parsnip', 'rms', 'rstanarm', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘anovaES.Rmd’ using rmarkdown
--- finished re-building ‘anovaES.Rmd’

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

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

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

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

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

Quitting from lines 235-244 [unnamed-chunk-13] (from_test_statistics.Rmd)
Error: processing vignette 'from_test_statistics.Rmd' failed with diagnostics:
could not find function "emmeans"
--- failed re-building ‘from_test_statistics.Rmd’

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'pbkrtest', 'heplots', 'car', 'alr4', 'robustlmm'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Packages required but not available:
  'dendextend', 'fungible', 'GGally', 'ggplot2', 'ggpubr', 'igraph',
  'network', 'qgraph', 'semPlot', 'sna'

Package suggested but not available for checking: ‘progress’

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Packages required but not available:
  'dplyr', 'tibble', 'tidygraph', 'srvyr', 'tidyr', 'purrr', 'pillar'

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'forcats', 'stringr', 'purrr', 'tidyr',
  'kableExtra', 'tibble', 'igraph', 'tidygraph', 'readr', 'readxl'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'vegdata', 'testthat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘eHOF.Rnw’ using knitr

Quitting from lines 34-43 [prep] (eHOF.Rnw)
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
there is no package called 'vegdata'
--- failed re-building ‘eHOF.Rnw’

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

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

Packages suggested but not available for checking:
  'logistf', 'medExtractR', 'ggplot2'

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

Package suggested but not available for checking: ‘devtools’

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

Package suggested but not available for checking: ‘plotly’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘eiCircles-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.BPF
> ### Title: Graphical representation of a RxC ecological inference (vote
> ###   transfer) matrix
> ### Aliases: plot.BPF
> 
> ### ** Examples
> 
> votes1 <- structure(list(P1 = c(16L, 4L, 13L, 6L, 1L, 16L, 6L, 17L, 48L, 14L),
+                          P2 = c(8L, 3L, 0L, 5L, 1L, 4L, 7L, 6L, 28L, 8L),
+                          P3 = c(38L, 11L, 11L, 3L, 13L, 39L, 14L, 34L, 280L, 84L),
+                          P4 = c(66L, 5L, 18L, 39L, 30L, 57L, 35L, 65L, 180L, 78L),
+                          P5 = c(14L, 0L, 5L, 2L, 4L, 21L, 6L, 11L, 54L, 9L),
+                          P6 = c(8L, 2L, 5L, 3L, 0L, 7L, 7L, 11L, 45L, 17L),
+                          P7 = c(7L, 3L, 5L, 2L, 3L, 17L, 7L, 13L, 40L, 8L)),
+                          row.names = c(NA, 10L), class = "data.frame")
> votes2 <- structure(list(C1 = c(2L, 1L, 2L, 2L, 0L, 4L, 0L, 4L, 19L, 14L),
+                          C2 = c(7L, 3L, 1L, 7L, 2L, 5L, 3L, 10L, 21L, 6L),
+                          C3 = c(78L, 7L, 28L, 42L, 28L, 84L, 49L, 85L, 260L, 100L),
+                          C4 = c(56L, 14L, 20L, 7L, 19L, 54L, 22L, 50L, 330L, 91L),
+                          C5 = c(14L, 3L, 6L, 2L, 3L, 14L, 8L, 8L, 45L, 7L)),
+                          row.names = c(NA, 10L), class = "data.frame")
> example <- BPF(votes1, votes2)
> p <- plot(example, show.plot = FALSE)
Error: Package ggplot2 needed for this function to work. Please install it.
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
BPF 4.827  0.013   6.747
Package suggested but not available for checking: ‘igraph’
Package required but not available: ‘tibble’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tidyselect', 'stringr', 'ggplot2', 'ggmap',
  'viridis'

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

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: ‘igraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'lme4', 'blme', 'reshape2', 'optimx', 'readxl', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'purrr', 'DALEX', 'ggrepel', 'ggiraphExtra', 'iBreakDown',
  'tidyr'

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

Packages suggested but not available for checking:
  'ggquiver', 'ggspatial', 'ggthemes'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) docs_delete_by_query.Rd:47: Lost braces; missing escapes or markup?
    47 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
checkRd: (-1) docs_update_by_query.Rd:48: Lost braces; missing escapes or markup?
    48 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'haven', 'readr'

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) electData.Rd:16: Lost braces; missing escapes or markup?
    16 | Variables: \code{id}  = {identification number},
       |                         ^
checkRd: (-1) electData.Rd:17: Lost braces; missing escapes or markup?
    17 | \code{state} = {state}, \code{age} = age in years on a shifted scale (current age minus 70),
       |                ^
checkRd: (-1) summary.elect.Rd:25: Lost braces; missing escapes or markup?
    25 |  TRUE for output on start-state totals e_{r.} (for \code{S}>0)
       |                                          ^
Packages required but not available: 'furrr', 'purrr', 'slippymath'

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

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

Packages suggested but not available for checking:
  'rgbif', 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) prepareInitsLM.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'devtools', 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) elliptic-package.Rd:92: Lost braces
    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'reshape2', 'lubridate'

Package suggested but not available for checking: ‘ggplot2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) elo.run.Rd:80: Lost braces
    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
       |                                            ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'EloRating', 'rstan', 'aniDom'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘shiny.i18n’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'mediation', 'minfi', 'ggplot2',
  'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

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

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

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'Microsoft365R'

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

Packages suggested but not available for checking:
  'dials', 'ggplot2', 'hardhat', 'keras', 'lme4', 'modeldata',
  'rstanarm', 'tensorflow', 'testthat'

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

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

Package suggested but not available for checking: ‘car’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'R2jags', 'testthat'
checkRd: (-1) NEWS.Rd:194: Lost braces; missing escapes or markup?
   194 |             \item added {d,r}betabinom
       |                         ^
Packages required but not available:
  'ggplot2', 'reshape2', 'stringr', 'HLMdiag', 'readODS', 'saeRobust'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-13 (Debian 13.2.0-25) 13.2.0’
License stub is invalid DCF.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'tibble', 'tidyr', 'stringr'

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

Packages suggested but not available for checking:
  'testthat', 'bootnet', 'qgraph', 'cglasso'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) EmiStatR-methods.Rd:86: Lost braces; missing escapes or markup?
    86 | execute {EmiStatR} function
       |         ^
checkRd: (-1) input-class.Rd:136: Lost braces; missing escapes or markup?
   136 |     \item{EmiStatR}{\code{signature(x = "input")}: execute {EmiStatR} function }
       |                                                            ^
Packages suggested but not available for checking: 'testthat', 'reshape2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'rdflib'
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'taxadb', 'tibble', 'testthat', 'EML'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bayesplot', 'brms', 'car', 'ggplot2', 'mediation', 'pbkrtest',
  'lme4', 'lmerTest', 'testthat', 'tibble'

Packages which this enhances but not available for checking:
  'CARBayes', 'geepack', 'mice', 'rstanarm'
Running examples in ‘emmeans-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: auto.noise
> ### Title: Auto Pollution Filter Noise
> ### Aliases: auto.noise
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # (Based on belief that noise/10 is in decibel units)
> noise.lm <- lm(noise/10 ~ size * type * side, data = auto.noise)
> 
> # Interaction plot of predictions
> emmip(noise.lm, type ~ size | side)
Error in .requireNS("ggplot2", "The 'ggplot' engine requires the 'ggplot2' package be installed.") : 
  The 'ggplot' engine requires the 'ggplot2' package be installed.
Calls: emmip -> emmip.default -> .requireNS -> fail
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GGally', 'ggplot2'
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) macacaModels.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) macacaModels.Rd:10-11: Lost braces in \itemize; meant \describe ?
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr', 'purrr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) WRegTest.Rd:43: Lost braces
    43 | For ordinary least squares estimator, \code{psifun} should be the identity function psifun <- function(t){t}.
       |                                                                                                          ^
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                              ^
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                                            ^
Package required but not available: ‘ACDm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘hopbyhop’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'robustHD'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ENMeval', 'ggpubr', 'forcats'

Packages suggested but not available for checking:
  'testthat', 'hypervolume', 'ecospat', 'caret', 'CalibratR',
  'reshape2', 'vip', 'pdp', 'viridis', 'progress'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'networkD3'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘GLMs.Rmd’ using rmarkdown

Quitting from lines 50-69 [unnamed-chunk-2] (GLMs.Rmd)
Error: processing vignette 'GLMs.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘GLMs.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dendextend', 'ggplot2', 'ggdendro'

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

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

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

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

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:
  'dplyr', 'stringr', 'ggplot2', 'reshape2', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'ggforce', 'qwraps2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggrepel', 'hrbrthemes', 'tidyverse', 'dplyr', 'tidyr',
  'tibble'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) entropy.Dirichlet.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:42: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'dplyr', 'readr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'stringr', 'testthat'
Running ‘test_envDocument.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'animation', 'mixtools', 'igraph'

Packages suggested but not available for checking:
  'testthat', 'xcms', 'MSnbase', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘enviPat/libs/enviPat.so’:
  Found non-API call to R: ‘SETLENGTH’

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: ‘concaveman’

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httr2’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘Hmisc’

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

Packages suggested but not available for checking:
  'httr2', 'ipaddress', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'broom', 'dplyr', 'ggplotify', 'magick', 'ggplot2', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > #*****************************************
  > #
  > # (C) Copyright IBM Corp. 2017
  > # Author: Ernesto Arandia & Bradley J Eck
  > #
  > #*****************************************
  > 
  > 
  > 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘Net1-fromR.inp’
Packages suggested but not available for checking:
  'ggcorrplot', 'tidyverse', 'reshape2', 'matlabr', 'testthat'
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                           ^
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                                        ^
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epca.Rmd’ using knitr

Quitting from lines 13-19 [setup] (epca.Rmd)
Error: processing vignette 'epca.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘epca.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'readxl', 'janitor', 'furrr', 'lubridate',
  'tsibble', 'stringr', 'fabletools', 'feasts', 'tibble', 'forcats',
  'readr', 'ggplot2'

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

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

Packages suggested but not available for checking:
  'testthat', 'lubridate', 'ggplot2', 'readr', 'forcats', 'httptest'

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rio', 'dplyr', 'tidyr', 'ggplot2', 'stringr', 'tidyselect', 'purrr',
  'tibble', 'janitor'

Packages suggested but not available for checking:
  'testthat', 'haven', 'readxl', 'readODS', 'feather', 'arrow',
  'ggtext', 'ggdist', 'spsUtil', 'ggh4x'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'dplyr', 'rvest', 'tidyr', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'readr', 'tibble', 'usethis'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Packages required but not available: 'odbc', 'purrr', 'readr', 'stringr'

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

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

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

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

Packages suggested but not available for checking: 'ggridges', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'epicontacts', 'ggmap', 'ggplot2', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'cowplot', 'dplyr', 'forcats', 'ggplot2', 'Hmisc',
  'patchwork', 'purrr', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'furrr', 'ggsci', 'testthat'

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

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'devtools', 'usethis', 'pkgdown', 'styler',
  'igraph', 'stringr', 'dplyr', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'testthat', 'ggpubr'
Running examples in ‘EpiInvert-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EpiIndicators
> ### Title: 'EpiIndicators'
> ### Aliases: EpiIndicators
> 
> ### ** Examples
> 
> ## load data of epidemiological indicators obtained from the World in data
> ## organization
> data("owid")
> 
> ## Filter the data to get France epidemiological indicators
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'forcats', 'tidyr', 'tibble', 'tidyselect', 'ggplot2'

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

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

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

Packages suggested but not available for checking:
  'forecast', 'imputeTS', 'lme4', 'statnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'forecast', 'imputeTS', 'lme4', 'statnet'
Packages required but not available:
  'networkDynamic', 'tergm', 'ergm', 'ergm.ego', 'egor', 'network',
  'ggplot2', 'tibble', 'dplyr', 'networkLite'

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'patchwork', 'posterior', 'purrr', 'rstan'

Packages suggested but not available for checking:
  'cmdstanr', 'precommit', 'testthat', 'usethis'

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

Package suggested but not available for checking: ‘testthat’

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

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

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

Packages suggested but not available for checking:
  'lme4', 'demography', 'popEpi', 'tidyr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
Packages required but not available:
  'devtools', 'tidyverse', 'stringr', 'tibble', 'caret'

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

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

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

Package suggested but not available for checking: ‘ggplot2’

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

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'MM4LMM', 'purrr', 'stringr'

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

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'incidence', 'ggplot2', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'emayili', 'ggplot2', 'janitor', 'plotly', 'rtweet',
  'readxl', 'stringr', 'tibble', 'tidyverse', 'tidytext'

Package suggested but not available for checking: ‘taskscheduleR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'netplot', 'igraph'
File ‘epiworldR/libs/epiworldR.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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: 'ggplot2', 'plotly'

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'testthat', 'TopKLists', 'stringr', 'cowplot'

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

Packages suggested but not available for checking:
  'dbplyr', 'dplyr', 'shinytest2', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright 2019-2019 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of epsiwal.
  > #
  > # epsiwal is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU Lesser General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # epsiwal is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU Lesser General Public License for more details.
  > #
  > # You should have received a copy of the GNU Lesser General Public License
  > # along with epsiwal.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2019-06-10
  > # Copyright: Steven E. Pav, 2019-2019
  > # Author: Steven E. Pav
  > # Comments: Steven E. Pav
  > 
  > # because Hadley says it should be like this.
  > # see https://github.com/hadley/devtools/wiki/Testing
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tibble', 'dplyr', 'tidyr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'testthat', 'readxl', 'ggplot2', 'ggiraph', 'ggiraphExtra', 'FSA'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eq5d.Rmd’ using rmarkdown

Quitting from lines 145-156 [eq5dcf] (eq5d.Rmd)
Error: processing vignette 'eq5d.Rmd' failed with diagnostics:
there is no package called 'readxl'
--- failed re-building ‘eq5d.Rmd’

--- re-building ‘eq5d_nice_dsu.Rmd’ using rmarkdown
--- finished re-building ‘eq5d_nice_dsu.Rmd’

SUMMARY: processing the following file failed:
  ‘eq5d.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'stringr', 'tidyr'

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

Quitting from lines 84-88 [unnamed-chunk-7] (equateIRT_tutorial.Rmd)
Error: processing vignette 'equateIRT_tutorial.Rmd' failed with diagnostics:
there is no package called 'sna'
--- failed re-building ‘equateIRT_tutorial.Rmd’

--- re-building ‘equateIRT_paper.Rnw’ using Sweave
Warning: Argument mod1 is deprecated; please use mods and which instead.
Warning: Argument mod2 is deprecated; please use mods and which instead.
Loading required package: MASS
Loading required package: msm
Loading required package: polycor
--- finished re-building 'equateIRT_paper.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'broom', 'broom.mixed'

Packages suggested but not available for checking:
  'forecast', 'ggplot2', 'latex2exp', 'lme4', 'testthat', 'texPreview',
  'gtsummary'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘PairedData’

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:
  'igraph', 'tibble', 'progress', 'furrr'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Tm.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:55-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:36-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:40-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:43-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:75-77: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'DiagrammeR', 'dplyr'

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

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 suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ergm', 'btergm', 'dplyr', 'sna', 'network'

Package suggested but not available for checking: ‘ergm.count’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ergm', 'egor', 'network', 'purrr', 'tibble', 'dplyr'

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘sna’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'network', 'purrr', 'tibble'

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

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

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

Packages suggested but not available for checking:
  'sna', 'testthat', 'ergm.count', 'networkLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'EpiEstim', 'ggplot2', 'lubridate', 'patchwork', 'stringr',
  'tibble', 'tidyr'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ifa.Rd:16: Lost braces; missing escapes or markup?
    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
checkRd: (-1) ifa.Rd:17: Lost braces; missing escapes or markup?
    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
checkRd: (-1) ifa.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{iSB}{m x q matrix (diag(Psi)+BB')^{-1}B.}
       |                                         ^
checkRd: (-1) isqrtfa.Rd:15: Lost braces; missing escapes or markup?
    15 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then the function returns a matrix Omega such that Sigma^{-1} = Omega Omega'. Equivalently,
       |                                                                                                                       ^
Packages required but not available: 'ggplot2', 'plsVarSel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'vctrs', 'pillar', 'ggplot2', 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rjournal.Rmd’ using rmarkdown

Quitting from lines 97-123 [propagation] (rjournal.Rmd)
Error: processing vignette 'rjournal.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘rjournal.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'car', 'broom', 'dplyr', 'tidyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'readODS', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tidyselect', 'stringr', 'purrr', 'tibble',
  'ggplot2', 'trialr', 'DiagrammeR', 'viridis', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggdist', 'ggh4x', 'ggtext', 'ggbeeswarm', 'stringr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'colourpicker', 'testthat', 'tmap', 'viridis'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) festRidge.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{XtXlamIinv}{explicit value of (X'X + diag(penalty))^{-1}.  Useful
       |                                                           ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'kableExtra', 'lubridate', 'stringr',
  'tidyr'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
File ‘essentials/libs/essentials.so’:
  Found non-API call to R: ‘UNSET_S4_OBJECT’

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: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

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

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'brms', 'lme4', 'dplyr', 'tidyr', 'ggplot2', 'cowplot'

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

Package suggested but not available for checking: ‘JGL’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggh4x', 'ggplot2', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'margins', 'testthat', 'car'
Unknown package ‘margins’ in Rd xrefs
Running examples in ‘estimatr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lh_robust
> ### Title: Linear Hypothesis for Ordinary Least Squares with Robust
> ###   Standard Errors
> ### Aliases: lh_robust
> 
> ### ** Examples
> 
> 
> library(fabricatr)
> dat <- fabricate(
+   N = 40,
+   y = rpois(N, lambda = 4),
+   x = rnorm(N),
+   z = rbinom(N, 1, prob = 0.4),
+   clusterID = sample(1:4, 40, replace = TRUE)
+ )
> 
> # Default variance estimator is HC2 robust standard errors
> lhro <- lh_robust(y ~ x + z, data = dat, linear_hypothesis = "z + 2x = 0")
Loading required namespace: car
Failed with error:  ‘there is no package called ‘car’’
Error in loadNamespace(x) : there is no package called ‘car’
Calls: lh_robust ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘sleep.R’ [1s/1s]
  Comparing ‘sleep.Rout’ to ‘sleep.Rout.save’ ... OK
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'reshape2', 'ggplot2', 'testthat'

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

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) ETC-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:32: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'cowplot', 'dplyr', 'ggalluvial', 'ggplot2', 'ggridges', 'reshape2'

Packages suggested but not available for checking:
  'broom', 'tidyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'dbplyr', 'janitor', 'lubridate', 'readr', 'rvest',
  'tibble', 'usethis'

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

VignetteBuilder packages required for checking but not installed:
  'ggplot2', 'dplyr', 'dbplyr'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.dbi.ffdf
> ### Title: Read data from a DBI connection into an ffdf.
> ### Aliases: read.dbi.ffdf
> 
> ### ** Examples
> 
> require(ff)
> 
> ##
> ## Example query using data in sqlite
> ##
> require(RSQLite)
Loading required package: RSQLite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘RSQLite’
> dbfile <- system.file("smalldb.sqlite3", package="ETLUtils")
> drv <- dbDriver("SQLite")
Error in dbDriver("SQLite") : could not find function "dbDriver"
Execution halted
Packages suggested but not available for checking: 'ggplot2', 'geepack'
Packages required but not available: 'dplyr', 'rvest', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'brainGraph', 'fda.usc', 'igraph', 'NetworkDistance', 'TDA'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'did', 'gt', 'ggplot2'
Running ‘tinytest.R’ [8s/11s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("etwfe")
  + }
  
  test_baker.R..................    0 tests    
  test_baker.R..................    0 tests    
  test_baker.R..................    0 tests    
  test_baker.R..................    0 tests    
  test_baker.R..................    0 tests    
  test_baker.R..................    5 tests [0;32mOK[0m [0;34m10.0s[0m
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'did'
  Calls: <Anonymous> ... lapply -> FUN -> eval -> eval -> data -> find.package
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘etwfe.Rmd’ using rmarkdown

Quitting from lines 114-117 [unnamed-chunk-2] (etwfe.Rmd)
Error: processing vignette 'etwfe.Rmd' failed with diagnostics:
there is no package called 'did'
--- failed re-building ‘etwfe.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'patchwork', 'tidyr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'RSQLite', 'arrow', 'CommonDataModel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'rvest', 'stringr', 'readr'

Packages suggested but not available for checking:
  'tidytext', 'purrr', 'ggplot2', 'ggiraph', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'readr'
Packages required but not available:
  'dplyr', 'httr2', 'ISOweek', 'lubridate', 'readr', 'RefManageR',
  'regions', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'FRESA.CAD', 'NMF'
checkRd: (-1) FuzzyCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "fcm {ppclust}"
       |                                                       ^
checkRd: (-1) pamCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "pam {cluster}"
       |                                                       ^
Running examples in ‘Evacluster-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nmfCluster
> ### Title: Non-negative matrix factorization (NMF)
> ### Aliases: nmfCluster
> 
> ### ** Examples
> 
> library(datasets)
> data(iris)
> 
> rndSamples <- sample(nrow(iris),100)
> trainData <- iris[rndSamples,]
> testData <- iris[-rndSamples,]
> 
> cls <- nmfCluster(trainData[,1:4],rank=3)
Error in loadNamespace(x) : there is no package called ‘NMF’
Calls: nmfCluster ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'dplyr', 'caret', 'forcats', 'ggdist', 'ggplot2', 'ggthemes',
  'haven', 'purrr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > 
  > suppressWarnings(library(testthat))
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown

Quitting from lines 85-90 [unnamed-chunk-4] (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building ‘Overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'car', 'dplyr', 'ggcorrplot', 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'MetaUtility', 'dplyr'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'ggpubr', 'kableExtra', 'tibble', 'testthat'

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

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

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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: ‘dplyr’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) colplot.Rd:52: Lost braces
    52 | \item{legend}{should a legend be added? Defaults to code{FALSE}}
       |                                                         ^
checkRd: (-1) colplot.Rd:56: Lost braces
    56 | \item{legend.pretty}{logical: should the legend values produced by \[base]{pretty}? Othewrwise they are exact. Defaults to \code{TRUE}}
       |                                                                           ^
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) glr.Rd:5: Lost braces
     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
checkRd: (-1) glr.Rd:34: Lost braces
    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
Packages required but not available: 'rstan', 'rstanarm', 'loo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggdist', 'meta', 'EmpiricalCalibration',
  'Cyclops'

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fmgammagpd.Rd:183: Lost braces; missing escapes or markup?
   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
checkRd: (-1) fmgammagpdcon.Rd:181: Lost braces; missing escapes or markup?
   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
checkRd: (-1) kernels.Rd:87: Lost braces
    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
Packages required but not available: 'geiger', 'phytools'

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'deeptime', 'ggplot2', 'ggrepel', 'ggtree', 'patchwork',
  'treeio', 'devtools'

Package suggested but not available for checking: ‘kableExtra’

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:
  'cowplot', 'dplyr', 'ggplot2', 'lubridate', 'plotly', 'purrr',
  'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 87-98 [plot predictions] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- 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:
  'dplyr', 'lubridate', 'purrr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘exact2x2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
Specified C++14: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vig1_population.Rmd’ using rmarkdown

Quitting from lines 39-43 [setup] (vig1_population.Rmd)
Error: processing vignette 'vig1_population.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘vig1_population.Rmd’

--- re-building ‘vig2_categorical.Rmd’ using rmarkdown

Quitting from lines 36-40 [setup] (vig2_categorical.Rmd)
Error: processing vignette 'vig2_categorical.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘vig2_categorical.Rmd’

SUMMARY: processing the following files failed:
  ‘vig1_population.Rmd’ ‘vig2_categorical.Rmd’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ExactData’
Packages required but not available:
  'purrr', 'readr', 'roxygen2', 'strex', 'stringr', 'styler', 'usethis'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘magick’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'readxl', 'stringr', 'tidyr'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tidyr', 'lubridate', 'ggplot2'

Package suggested but not available for checking: ‘tidycensus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ipaddress', 'janitor', 'lubridate', 'stringr', 'tidyr',
  'tidyselect'

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘testthat’

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:
  'tidyr', 'dplyr', 'ggplot2', 'kableExtra', 'rio'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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:
  'RSQLite', 'readxl', 'tibble', 'lubridate', 'dplyr', 'weaana',
  'tidyr', 'tidyverse', 'reshape2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'smoof', 'cec2013'
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:42: Lost braces
    42 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
checkRd: (-1) ccF.Rd:41: Lost braces
    41 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'huxtable', 'stringr', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DESeq2', 'ggplot2', 'ggsci'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cvms', 'dplyr', 'egg', 'ggplot2', 'ggpmisc', 'ggpubr', 'plotly',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'cowplot', 'broom', 'iml', 'forcats', 'mlr3viz', 'plotROC',
  'reshape2', 'precrec'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggridges', 'lemon', 'mediation', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'plotly', 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

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

Packages suggested but not available for checking:
  'FactoMineR', 'GDAtools', 'testthat'

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'flora', 'tibble', 'cowplot', 'PupillometryR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
Package required but not available: ‘forecast’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘optimx’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'hms', 'ggplot2', 'testthat', 'tibble', 'tidyr', 'viridis'
Running examples in ‘extras-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: numericise
> ### Title: Numericise (or Numericize)
> ### Aliases: numericise numericize numericise.logical numericise.integer
> ###   numericise.double numericise.factor numericise.Date
> ###   numericise.POSIXct numericise.hms numericise.matrix numericise.array
> ###   numericise.data.frame
> 
> ### ** Examples
> 
> 
> # logical
> numericise(TRUE)
[1] 1
> numericise(matrix(c(TRUE, FALSE), nrow = 2))
     [,1]
[1,]    1
[2,]    0
> 
> # integer
> numericise(2L)
[1] 2
> 
> # double
> numericise(c(1, 3))
[1] 1 3
> 
> # factor
> numericise(factor(c("c", "a")))
[1] 2 1
> 
> # Date
> numericise(as.Date("1972-01-01"))
[1] 730
> 
> # POSIXct
> numericise(as.POSIXct("1972-01-01", tz = "UTC"))
[1] 63072000
> 
> # hms
> numericise(hms::as_hms("00:01:03"))
Error in loadNamespace(x) : there is no package called ‘hms’
Calls: numericise ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘beta-binomial-deviance-residuals.Rmd’ using rmarkdown

Quitting from lines 11-21 [unnamed-chunk-1] (beta-binomial-deviance-residuals.Rmd)
Error: processing vignette 'beta-binomial-deviance-residuals.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘beta-binomial-deviance-residuals.Rmd’

--- re-building ‘deviance-residuals.Rmd’ using rmarkdown
--- finished re-building ‘deviance-residuals.Rmd’

SUMMARY: processing the following file failed:
  ‘beta-binomial-deviance-residuals.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MatIn.Rd:6: Lost braces
     6 | Computation of aggregation matrices for generalized interactions that are used in code{\link{extRC}} to estimate extended RC models.
       |                                                                                       ^
checkRd: (-1) plot.Rd:5: Lost braces
     5 | \description{It plots the output of code{\link{extRC}} function for a vector of lambda values.}
       |                                         ^
checkRd: (-1) print.Rd:5: Lost braces
     5 | \description{Given the output of code{\link{extRC}} function, it is written in a readable form.}
       |                                      ^
checkRd: (-1) summary.Rd:5: Lost braces
     5 | \description{Summary method for the output of code{\link{extRC}} function.}
       |                                                   ^
Packages required but not available: 'nloptr', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'purrr', 'tibble', 'tidyr',
  'progress'

Packages suggested but not available for checking:
  'exuberdata', 'forcats', 'stringr', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forestmodel', 'ggplot2', 'purrr', 'tibble'

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'purrr', 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'ggrepel', 'testthat', 'tibble', 'tidyr', 'tsibble', 'tsibbledata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'ggplot2', 'lme4', 'reshape2', 'stringr'

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

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

Packages suggested but not available for checking:
  'dplyr', 'yardstick', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'httr2', 'janitor', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'httptest2', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'testthat', 'devtools'
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'NMF', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fabletools', 'ATAforecasting', 'tibble', 'dplyr', 'tsibble',
  'distributional', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fabletools', 'fable', 'dplyr', 'tsibble', 'tibble', 'tidyr',
  'distributional', 'lubridate', 'stringr', 'tsibbledata'

Packages suggested but not available for checking:
  'feasts', 'forecast', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fabletools', 'tsibble', 'lubridate', 'prophet', 'dplyr',
  'distributional'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fabletools', 'dplyr', 'tsibble', 'tibble', 'tidyr', 'distributional'

Packages suggested but not available for checking:
  'feasts', 'forecast', 'testthat', 'tsibbledata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tsibble', 'tibble', 'ggplot2', 'tidyselect', 'dplyr', 'tidyr',
  'vctrs', 'distributional', 'ggdist'

Packages suggested but not available for checking:
  'fable', 'pillar', 'feasts', 'testthat', 'tsibbledata', 'lubridate'

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

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

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: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'usethis', 'stringr', 'tidyr', 'purrr', 'janitor', 'readr',
  'readxl', 'haven', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'stringr', 'snakecase'

Packages suggested but not available for checking:
  'magick', 'ggplot2', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rugarch', 'HH'
checkRd: (-1) fmCov.Rd:37: Lost braces; missing escapes or markup?
    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
checkRd: (-1) plot.ffm.Rd:82: Lost braces; missing escapes or markup?
    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
checkRd: (-1) summary.ffm.Rd:39: Lost braces; missing escapes or markup?
    39 | Returned object is of class {summary.ffm}.
       |                             ^
Packages suggested but not available for checking: 'HH', 'rugarch'
Packages suggested but not available for checking: 'tibble', 'dplyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘factiv.Rmd’ using rmarkdown

Quitting from lines 84-85 [tidy] (factiv.Rmd)
Error: processing vignette 'factiv.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘factiv.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dendextend', 'FactoMineR', 'ggpubr', 'reshape2',
  'ggrepel', 'tidyr'

Package suggested but not available for checking: ‘igraph’

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

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

Packages suggested but not available for checking: 'missMDA', 'Factoshiny'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Package required but not available: ‘dplyr’

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

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FactoMineR', 'FactoInvestigate', 'ggplot2', 'colourpicker',
  'ggrepel', 'missMDA'

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

Packages suggested but not available for checking:
  'testthat', 'caret', 'FuzzyDBScan', 'factoextra', 'patchwork'

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

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) happy.Rd:14: Lost braces
    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
Package suggested but not available for checking: ‘testthat’
Running ‘test_all.R’ [0s/1s]
Running the tests in ‘tests/test_all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'ggplot2', 'cowplot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'tidyjson', 'igraph', 'dplyr'

Package suggested but not available for checking: ‘testthat’

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

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

Packages suggested but not available for checking:
  'testthat', 'ggdendro', 'ggrepel'

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

Package suggested but not available for checking: ‘testthat’

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Ecdat', 'ggplot2', 'qvalue', 'randomForestSRC', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'lubridate', 'VirtualPop'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘future.batchtools’
checkRd: (-1) pi0FAMT.Rd:18: Lost braces
    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'sensitivity', 'igraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggfun', 'httr2', 'purrr', 'SSEparser'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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: ‘readr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages required but not available: 'readr', 'tibble', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dbplyr', 'dplyr', 'tidyr', 'tibble', 'readr', 'stringr', 'lubridate'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'ggpubr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'forecast', 'progress', 'RcppClock', 'testthat'

Packages suggested but not available for checking:
  'breakfast', 'dplyr', 'ggplot2', 'lubridate', 'RcppClock',
  'reshape2', 'stepR', 'testthat', 'VARDetect'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6
< NULL
---
> All Done!
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'lme4', 'cAIC4', 'dplyr', 'refund', 'stringr', 'progress', 'ggplot2',
  'lmeresampler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'cowplot'
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_fastglmpca.Rmd’ using rmarkdown

Quitting from lines 30-34 [load-pkgs] (intro_fastglmpca.Rmd)
Error: processing vignette 'intro_fastglmpca.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘intro_fastglmpca.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'testthat', 'caret'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'caret', 'timeROC'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘coxKM’
checkRd: (-1) KITdesign.Rd:36: Lost braces; missing escapes or markup?
    36 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) KITkernel.Rd:51: Lost braces; missing escapes or markup?
    51 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) geno.Rd:19: Lost braces; missing escapes or markup?
    19 |                 Must be one of {'ibs', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) geno.Rd:31: Lost braces; missing escapes or markup?
    31 |                      {'add', 'dom', 'rec'} indicating additive,
       |                      ^
checkRd: (-1) nongeno.Rd:14: Lost braces; missing escapes or markup?
    14 |                 Must be one of {'interactive', 'linear', 'quadratic'}.
       |                                ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'stringr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                     ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_NAMED’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
File ‘fastMatMR/libs/fastMatMR.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'tidygraph'

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

Package suggested but not available for checking: ‘testthat’

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

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

Packages suggested but not available for checking:
  'ggformula', 'mosaicCalc', 'tidyr', 'readr', 'faraway', 'Hmisc',
  'car', 'alr4', 'BradleyTerry2'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'furrr', 'ggplot2', 'ggrepel', 'RSQLite', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'dplyr', 'ggplot2', 'plater', 'purrr', 'readxl', 'stringr',
  'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AmesHousing', 'shapviz', 'tibble'
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'progress', 'ggplot2', 'ggrepel', 'cowplot', 'plotly'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DESeq2’
Packages suggested but not available for checking:
  'dplyr', 'haven', 'testthat', 'tibble', 'tidyr', 'vctrs'
Running examples in ‘fauxnaif-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: na_if_in
> ### Title: Convert values to NA
> ### Aliases: na_if_in na_if_not
> 
> ### ** Examples
> 
> x <- sample(c(1:5, 99))
> # We can replace 99...
> # ... explicitly
> na_if_in(x, 99)
[1]  1  4  3 NA  2  5
> # ... by specifying values to keep
> na_if_not(x, 1:5)
[1]  1  4  3 NA  2  5
> # ... or by using a formula
> na_if_in(x, ~ . > 5)
[1]  1  4  3 NA  2  5
> 
> messy_string <- c("abc", "", "def", "NA", "ghi", 42, "jkl", "NULL", "mno")
> # We can replace unwanted values...
> # ... one at a time
> clean_string <- na_if_in(messy_string, "")
> clean_string <- na_if_in(clean_string, "NA")
> clean_string <- na_if_in(clean_string, 42)
> clean_string <- na_if_in(clean_string, "NULL")
> clean_string
[1] "abc" NA    "def" NA    "ghi" NA    "jkl" NA    "mno"
> # ... or all at once
> na_if_in(messy_string, "", "NA", "NULL", 1:100)
[1] "abc" NA    "def" NA    "ghi" NA    "jkl" NA    "mno"
> na_if_in(messy_string, c("", "NA", "NULL", 1:100))
[1] "abc" NA    "def" NA    "ghi" NA    "jkl" NA    "mno"
> na_if_in(messy_string, list("", "NA", "NULL", 1:100))
[1] "abc" NA    "def" NA    "ghi" NA    "jkl" NA    "mno"
> # ... or using a clever formula
> grepl("[a-z]{3,}", messy_string)
[1]  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE
> na_if_not(messy_string, ~ grepl("[a-z]{3,}", .))
[1] "abc" NA    "def" NA    "ghi" NA    "jkl" NA    "mno"
> 
> # na_if_in() is particularly useful inside dplyr::mutate
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fauxnaif.Rmd’ using rmarkdown
Error: processing vignette 'fauxnaif.Rmd' failed with diagnostics:
Printing 'tibble' without 'tibble' package available
--- failed re-building ‘fauxnaif.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
checkRd: (-1) Error.Rd:33-45: Lost braces
    33 |   \item \code{do(response, mssg)} {
       |                                   ^
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lme4', 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'roxygen2', 'cowplot', 'ggExtra', 'purrr',
  'broom', 'broom.mixed', 'lmerTest', 'kableExtra', 'readr',
  'patchwork'

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

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

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) FBN.histogramMaxima.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.histogramMaxima.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBN.kmeans.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FBNormalization.Rd:40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) fbad_copy_ad.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_ad.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_adset.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_adset.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
checkRd: (-1) fbad_copy_campaign.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{status_option}{(string) enum {ACTIVE, PAUSED, INHERITED_FROM_SOURCE}}
       |                                    ^
checkRd: (-1) fbad_copy_campaign.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{rename_strategy}{(string) enum {DEEP_RENAME, ONLY_TOP_LEVEL_RENAME, NO_RENAME}}
       |                                      ^
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘BayesFactor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'POSetR', 'stringr', 'tibble',
  'tidyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'cowplot', 'dplyr', 'Hmisc'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘fcl/libs/fcl.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘FCO.Rmd’ using rmarkdown

Quitting from lines 11-18 [unnamed-chunk-1] (FCO.Rmd)
Error: processing vignette 'FCO.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘FCO.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'DataVisualizations'

Packages suggested but not available for checking:
  'ADPclust', 'DatabionicSwarm', 'subspace', 'plotly',
  'ProjectionBasedClustering', 'GeneralizedUmatrix', 'mstknnclust',
  'densityClust', 'Spectrum', 'reshape2', 'clustrd', 'smacof',
  'dendextend', 'VarSelLCM', 'mixtools', 'yardstick', 'igraph',
  'leiden', 'clustMixType', 'NetworkToolbox', 'ClusterR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘purrr’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
checkRd: (-1) fcr-package.Rd:15: Lost braces; missing escapes or markup?
    15 | Let $y_{ij}$ denote some outcome measured at
       |        ^
checkRd: (-1) fcr-package.Rd:16: Lost braces; missing escapes or markup?
    16 | $t_{ij}$ on the functional domain (e.g. time) for subject $i$ at observation
       |    ^
checkRd: (-1) fcr-package.Rd:29: Lost braces; missing escapes or markup?
    29 | Initially, a model is fit without $b_i(t_{ij})$. Using the residuals from this initial fit,
       |                                          ^
checkRd: (-1) fcr.Rd:13: Lost braces; missing escapes or markup?
    13 | The formula should only include terms not associated with the random function intercept b_i(t_{ij}). See Examples.}
       |                                                                                               ^
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fdasrvf', 'forcats', 'furrr', 'ggplot2', 'nloptr', 'purrr',
  'tibble', 'tidyr'

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                              ^
checkRd: (-1) simulation_model9.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{ci}{A vector of 2 values containing $c_{1i}$ and $c_{2i}$ in the contamination
       |                                                           ^
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fdapace', 'ggplot2', 'plotly', 'purrr', 'reshape2',
  'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
GNU make is a SystemRequirements.
Packages required but not available:
  'ggplot2', 'tibble', 'reshape2', 'patchwork', 'fdapace'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘latex2exp’
Package required but not available: ‘tolerance’

Package suggested but not available for checking: ‘testthat’

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

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 suggested but not available for checking:
  'fda', 'ggplot2', 'refund', 'testthat'
Note: skipping ‘FLAM_canada.Rnw’ due to unavailable dependencies: 'fda'
Note: skipping ‘FLAM_fuel.Rnw’ due to unavailable dependencies: 'fda'
Note: skipping ‘FLAM_viscosity.Rnw’ due to unavailable dependencies: 'fda'
Note: skipping ‘density-on-scalar_birth.Rnw’ due to unavailable dependencies:
  'fda'
Packages suggested but not available for checking:
  'ggplot2', 'reshape2', 'testthat', 'ggnewscale', 'ggforce'
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘benchmark.Rmd’ using rmarkdown
--- finished re-building ‘benchmark.Rmd’

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

Quitting from lines 258-296 [plot] (example.Rmd)
Error: processing vignette 'example.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘example.Rmd’

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

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

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

Quitting from lines 415-520 [validity-test] (validity.Rmd)
Error: processing vignette 'validity.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building ‘validity.Rmd’

SUMMARY: processing the following files failed:
  ‘example.Rmd’ ‘validity.Rmd’

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'car', 'caret', 'fds', 'questionr'

Package which this enhances but not available for checking: ‘NMF’

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:
  'Fgmutils', 'sqldf', 'randomcoloR', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘vert.txt’
Package required but not available: ‘ggplot2’

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

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.
checkRd: (-1) p.fdr.Rd:30: Lost braces
    30 | \item{adjust.method}{A string used to identify the p-value and false discovery rate adjustment method. Defaults to \code{BH}. Options are \code{BH}, \code{BY}, code{Bon},\code{Holm}, \code{Hoch}, and \code{Sidak}.}
       |                                                                                                                                                                     ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rainbow’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fabletools', 'tibble', 'tsibble', 'ggplot2', 'dplyr', 'tidyr',
  'vctrs', 'lubridate', 'slider'

Packages suggested but not available for checking:
  'tsibbledata', 'pillar', 'testthat', 'fable', 'ggrepel'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DatabaseConnector', 'Andromeda', 'dplyr', 'pillar', 'readr',
  'RSQLite'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mlr’
Found the following files/directories:
  ‘treesAll.txt’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'clustMixType', 'testthat', 'ClustImpute'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
Packages required but not available: 'ggplot2', 'GGally', 'panelView'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'stringr', 'igraph', 'lubridate',
  'progress', 'purrr', 'readr', 'arcgislayers'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'usethis', 'styler', 'rmapshaper'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rvest', 'tidyr', 'tidytext'

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'httr2', 'purrr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'httptest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'ggplot2', 'sae'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'gganimate', 'ggplot2', 'tibble', 'purrr', 'tourr',
  'stringr', 'ggrepel', 'ggforce', 'tidyr'

Packages suggested but not available for checking:
  'roxygen2', 'pkgdown', 'testthat', 'forcats', 'patchwork'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'readr', 'readxl', 'haven', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'forcats', 'ggdist', 'ggplot2', 'lubridate', 'purrr',
  'stringr', 'tibble', 'tidyr', 'vctrs', 'nloptr'

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fgeo.tool', 'lubridate', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'fgeo.plot', 'ggplot2', 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fgeo.tool', 'ggplot2', 'ggrepel', 'purrr', 'stringr'

Packages suggested but not available for checking:
  'fgeo.analyze', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fgeo.analyze', 'fgeo.plot', 'fgeo.tool', 'purrr'

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'network', 'sna'

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

Package suggested but not available for checking: ‘fda’

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

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'flexsurv', 'gapminder', 'GGally'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'viridis', 'desplot'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) FORTRAN.internal.Rd:50: Lost braces
    50 | \item{evlpoly}{evaluates a univariate polynomial. See code{fields.evlpoly}}
       |                                                           ^
checkRd: (-1) FORTRAN.internal.Rd:51: Lost braces
    51 | \item{evlpoly2}{ evaluates a multivariate polynomial. See code{fields.evlpoly2}}
       |                                                               ^
checkRd: (-1) registeredC.Rd:77: Lost braces
    77 | \item{addToDiagC}{ adds diagonal elements to a matrix. See code{mKrig}.}
       |                                                                ^
checkRd: (-1) sim.Krig.Rd:200-221: Lost braces
   200 | \code{simLocal.spatialProcess}{This function is
       |                               ^
checkRd: (-1) tim.colors.Rd:96: Lost braces
    96 | \item{\dots}{Additional plotting arguments to code{image.plot}}
       |                                                   ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'FIESTAutils', 'RSQLite', 'sqldf'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mase', 'RPostgres', 'RSQLite', 'sae', 'sqldf'

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'stringr', 'reshape2'

Packages suggested but not available for checking: 'tidyverse', 'latex2exp'

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

Packages suggested but not available for checking: 'phyloseq', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘filearray/libs/filearray.so’:
  Found non-API call to R: ‘R_PromiseExpr’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'janitor', 'purrr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'arrow', 'readr', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘RSQLite’
Packages suggested but not available for checking: 'io', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'purrr', 'strex'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'haven', 'httr2', 'readr', 'rvest', 'stringr', 'tidyr',
  'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'random.cdisc.data', 'testthat'
Running examples in ‘filters-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_filter
> ### Title: Apply a Filter to a Dataset or List of Datasets
> ### Aliases: apply_filter apply_filter.default apply_filter.data.frame
> ###   apply_filter.list
> 
> ### ** Examples
> 
> adsl <- random.cdisc.data::cadsl
Error in loadNamespace(x) : 
  there is no package called ‘random.cdisc.data’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'broom', 'dplyr', 'forcats', 'GGally', 'ggplot2', 'lme4', 'mice',
  'pillar', 'purrr', 'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'Hmisc', 'readr', 'rstan', 'survminer', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggplot2', 'ggtext', 'purrr', 'socialmixr',
  'testthat', 'tibble', 'tidyr'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/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
  > 
  > # nolint start
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lutz’

Packages suggested but not available for checking:
  'blob', 'readODS', 'readxl', 'RSQLite', 'testthat'

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘shinyFiles’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘run-all.R’ [0s/1s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tune', 'dials', 'dplyr', 'ggplot2', 'parsnip', 'purrr', 'tibble',
  'tidyr', 'tidyselect', 'vctrs', 'workflows'

Packages suggested but not available for checking:
  'BradleyTerry2', 'discrim', 'kknn', 'klaR', 'lme4', 'modeldata',
  'recipes', 'rsample', 'testthat', 'yardstick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Packages required but not available:
  'klaR', 'ggplot2', 'GGally', 'Rcmdr', 'car'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'igraph', 'network', 'yahoofinancer'
checkRd: (-1) fun-igraph_financial.Rd:34: Lost braces; missing escapes or markup?
    34 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_E_iterators.Rd:31: Lost braces; missing escapes or markup?
    31 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) igraph_v_iterators.Rd:29: Lost braces; missing escapes or markup?
    29 | The same result for both \code{igraph} and {igraph_financial} objects
       |                                            ^
checkRd: (-1) plot_igraph-methods.Rd:22: Lost braces
    22 | Methods to extend code{igraph}'s plotting functions to \code{igraph_financial} objects
       |                       ^
checkRd: (-1) plot_igraph-methods.Rd:19: Lost braces; missing escapes or markup?
    19 | For both \code{igraph} and {igraph_financial} objects, returns NULL invisibly. It is called to print the graph to any R device. (see method and \href{https://rdrr.io/cran/igraph/man/plot.igraph.html}{igraph::plot.igraph})
       |                            ^
Running examples in ‘FinNet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FF.graph
> ### Title: Easily represent a firm-firm (FF) network using the package
> ###   'igraph'
> ### Aliases: FF.graph
> 
> ### ** Examples
> 
> # Create a nice graph representation of the binary FF of
> # Berkshire Hataway's holdings based on common ownership
> data("firms_BKB")
> x <- FF.naive.ownership(firms_BKB)
> FF.graph(x = x, aesthetic = 'nice')
Error in loadNamespace(x) : there is no package called ‘igraph’
Calls: FF.graph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘workflow-igraph_financial.Rmd’ using knitr

Quitting from lines 70-72 [workflow_4] (workflow-igraph_financial.Rmd)
Error: processing vignette 'workflow-igraph_financial.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘workflow-igraph_financial.Rmd’

SUMMARY: processing the following file failed:
  ‘workflow-igraph_financial.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'ggraph', 'igraph', 'stringr',
  'textrank', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'modeltime', 'Cubist', 'dials', 'dplyr', 'feasts', 'hts',
  'lubridate', 'parsnip', 'purrr', 'recipes', 'rsample', 'rules',
  'snakecase', 'stringr', 'tibble', 'tidyr', 'tidyselect', 'timetk',
  'tune', 'vroom', 'workflows'

Packages suggested but not available for checking:
  'arrow', 'AzureStor', 'corrr', 'Microsoft365R', 'sparklyr',
  'testthat', 'vip'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'mockery'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘ggplot2’

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: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'dm', 'ggplot2', 'tidyr', 'DiagrammeR'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data-Model.Rmd’ using rmarkdown

Quitting from lines 18-27 [setup] (Data-Model.Rmd)
Error: processing vignette 'Data-Model.Rmd' failed with diagnostics:
there is no package called 'dm'
--- failed re-building ‘Data-Model.Rmd’

--- re-building ‘fishdata-examples.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (fishdata-examples.Rmd)
Error: processing vignette 'fishdata-examples.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘fishdata-examples.Rmd’

SUMMARY: processing the following files failed:
  ‘Data-Model.Rmd’ ‘fishdata-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available:
  'geiger', 'phytools', 'progress', 'rfishbase'

Package suggested but not available for checking: ‘gh’

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'geiger', 'hisse', 'phytools', 'rfishbase', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘community-analysis.Rmd’ using rmarkdown
--- finished re-building ‘community-analysis.Rmd’

--- re-building ‘comparative-analysis.Rmd’ using rmarkdown

Quitting from lines 41-48 [fishbase] (comparative-analysis.Rmd)
Error: processing vignette 'comparative-analysis.Rmd' failed with diagnostics:
there is no package called 'rfishbase'
--- failed re-building ‘comparative-analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘comparative-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'stringr', 'dplyr', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'janitor', 'lubridate', 'purrr', 'tibble', 'tidyr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'patchwork', 'viridis', 'ggthemes', 'varian',
  'paletteer', 'hms', 'rayshader', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fitConic.Rd:66-73: Lost braces
    66 | \code{parA }{vector of the six "ABCDEF" coefficients
       |             ^
checkRd: (-1) fitConic.Rd:67: Lost braces
    67 | \code{RSS }{'root sum square' figure of merit describing the relative fit quality}
       |            ^
checkRd: (-1) fitConic.Rd:68: Lost braces
    68 | \code{iters }{number of iterations at convergence}
       |              ^
checkRd: (-1) fitConic.Rd:69-71: Lost braces
    69 | \code{exitCode }{1 means ellipse, 2 means hyperbola, 3 means parabola.
       |                 ^
checkRd: (-1) rotateA.Rd:59: Lost braces; missing escapes or markup?
    59 | For \code{xyrot} {a Nx2 array of the x,y coordinates of the rotated data set. }
       |                  ^
Packages suggested but not available for checking:
  'mc2d', 'ggplot2', 'Hmisc'
Running examples in ‘fitdistrplus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CIcdfplot
> ### Title: Empirical cumulative distribution function with pointwise
> ###   confidence intervals on probabilities or on quantiles
> ### Aliases: CIcdfplot
> ### Keywords: distribution
> 
> ### ** Examples
> 
> # We choose a low number of bootstrap replicates in order to satisfy CRAN running times
> # constraint.
> # For practical applications, we recommend to use at least niter=501 or niter=1001.
> 
> if (requireNamespace ("ggplot2", quietly = TRUE)) {ggplotEx <- TRUE}
> 
> # (1) Fit of an exponential distribution
> #
> 
> set.seed(123)
> s1 <- rexp(50, 1)
> f1 <- fitdist(s1, "exp")
> b1 <- bootdist(f1, niter= 11) #voluntarily low to decrease computation time
> 
> # plot 95 percent bilateral confidence intervals on y values (probabilities)
> CIcdfplot(b1, CI.level= 95/100, CI.output = "probability")
> if (ggplotEx) CIcdfplot(b1, CI.level= 95/100, CI.output = "probability", plotstyle = "ggplot")
Error: object 'ggplotEx' not found
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'reshape2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'furrr', 'ggplot2', 'plotly', 'simlandr', 'SparseVFC',
  'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'ggplot2', 'ggthemes', 'reshape2', 'testthat', 'tibble', 'viridis'
Running ‘spelling.R’ [0s/0s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6
< NULL
---
> All Done!
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘gridlayout’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitode.Rnw’ using knitr

Quitting from lines 72-75 [pkgversions] (fitode.Rnw)
Error: processing vignette 'fitode.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘fitode.Rnw’

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

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'EnvStats', 'ExtDist', 'flexsurv', 'mc2d', 'nCDunnett', 'reliaR',
  'revdbayes', 'STAR'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'readr', 'rvest', 'stringr', 'tidyr',
  'tidyselect', 'tibble', 'httr2'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr', 'readr', 'tibble', 'stringr', 'broom',
  'patchwork', 'fivethirtyeightdata'
checkRd: (-1) food_world_cup.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) food_world_cup.Rd:75: Lost braces in \itemize; meant \describe ?
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Running examples in ‘fivethirtyeight-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ahca_polls
> ### Title: American Health Care Act Polls
> ### Aliases: ahca_polls
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # To convert data frame to tidy data (long) format, run:
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fivethirtyeight.Rmd’ using rmarkdown

Quitting from lines 13-63 [unnamed-chunk-1] (fivethirtyeight.Rmd)
Error: processing vignette 'fivethirtyeight.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘fivethirtyeight.Rmd’

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

Quitting from lines 26-34 [setup] (tame.Rmd)
Error: processing vignette 'tame.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘tame.Rmd’

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

SUMMARY: processing the following files failed:
  ‘fivethirtyeight.Rmd’ ‘tame.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'rb3', 'dplyr', 'testthat'

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.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'AER'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'purrr', 'lubridate', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘mlr’

Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'plotly', 'smoof', 'testthat'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flag_divide
> ### Title: Assignment of the weights for the multiple flags
> ### Aliases: flag_divide
> 
> ### ** Examples
> 
> flags <- tidyr::spread(test_data[, c(1:3)], key = time, value = flags)
Error in loadNamespace(x) : there is no package called ‘tidyr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘flagr_introduction.Rmd’ using rmarkdown

Quitting from lines 85-89 [hierarchy] (flagr_introduction.Rmd)
Error: processing vignette 'flagr_introduction.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘flagr_introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'mice', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'tibble', 'dplyr', 'purrr', 'tidyr', 'ggplot2', 'ggforce'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) ModelMixHMM-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMM}).
       |                                  ^
checkRd: (-1) ModelMixHMMR-class.Rd:31: Lost braces; missing escapes or markup?
    31 |         \code{smoothed} of class {StatMixHMMR}).
       |                                  ^
checkRd: (-1) summary.flamcv.rd:8: Lost braces
     8 | This function summarizes a call to code{\link{flamCV}} and identifies the tuning parameter chosen by cross-validation.
       |                                        ^
Package suggested but not available for checking: ‘forecast’
Running examples in ‘flap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flap
> ### Title: Forecast Linear Augmented Projection
> ### Aliases: flap
> 
> ### ** Examples
> 
> # Generate example data
> # T = 70, m = 20
> train <- matrix(rnorm(70 * 20),ncol = 20)
> 
> # Obtain the forecast and the residual of the original series
> mdl <- apply(train, 2, forecast::ets)
Error in loadNamespace(x) : there is no package called ‘forecast’
Calls: apply ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘igraph’

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.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
Packages required but not available:
  'ebnm', 'dplyr', 'stringr', 'tibble', 'tidyr', 'ggplot2'

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

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

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'purrr', 'rematch2', 'tibble', 'usethis'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) flex_dashboard.Rd:96: Lost braces; missing escapes or markup?
    96 | the `{.storyboard}` attribute to individual pages rather than using the
       |      ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'purrr', 'tibble', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fmp.Rd:45: Lost braces; missing escapes or markup?
    45 | If k = 0: (xi_1, ..., x_{C_i - 1}, omega)
       |                         ^
checkRd: (-1) fmp.Rd:47: Lost braces; missing escapes or markup?
    47 | If k = 1: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1)
       |                         ^
checkRd: (-1) fmp.Rd:49: Lost braces; missing escapes or markup?
    49 | If k = 2: (xi_1, ..., x_{C_i - 1}, omega, alpha1, tau1, alpha2, tau2)
       |                         ^
Packages suggested but not available for checking: 'Ecdat', 'lme4'
Package required but not available: ‘GJRM’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Error(s) in re-building vignettes:
  ...
--- re-building ‘main_vignette.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flexOR.Rcheck/vign_test/flexOR/vignettes/main_vignette_files/figure-html/apply_flexOR-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7832 bytes
Input file size = 8690 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7220
  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 = 7220

Output IDAT size = 7220 bytes (612 bytes decrease)
Output file size = 7298 bytes (1392 bytes = 16.02% decrease)


Quitting from lines 115-191 [plotly] (main_vignette.Rmd)
Error: processing vignette 'main_vignette.Rmd' failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘main_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'stringr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rstan', 'loo', 'bayesplot', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'relsurv', 'ggplot2', 'lubridate'

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'flexsurvcure', 'survminer', 'lubridate', 'testthat', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'broom', 'broom.mixed', 'doconv', 'ggplot2', 'lme4', 'magick',
  'pkgdown', 'testthat'
Running examples in ‘flextable-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_flextable.kmeans
> ### Title: Transform a 'kmeans' object into a flextable
> ### Aliases: as_flextable.kmeans
> 
> ### ** Examples
> 
> if (require("stats")) {
+   cl <- kmeans(scale(mtcars[1:7]), 5)
+   ft <- as_flextable(cl)
+   ft
+ }
Error in as_flextable.kmeans(cl) : 
  'broom' package should be installed to create a flextable from an object of type 'kmeans'.
Calls: as_flextable -> as_flextable.kmeans
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httr2', 'janitor'

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

Package suggested but not available for checking: ‘devtools’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dials', 'ggplot2', 'purrr', 'tibble', 'usethis'

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'caret'

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

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'dplyr', 'furrr', 'purrr', 'readr', 'rsample', 'stringr',
  'tibble', 'tidyr', 'vip'

Packages suggested but not available for checking:
  'adabag', 'arm', 'C50', 'Cubist', 'ggplot2', 'keras', 'kknn', 'klaR',
  'rrcovHD', 'shapviz'

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

Packages suggested but not available for checking:
  'testthat', 'esquisse', 'tidyselect', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) flowdata.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{Flow}{Water flow, in m^{3}/s}
       |                              ^
Packages required but not available: 'params', 'readr'

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

Packages which this enhances but not available for checking:
  'ggplot2', 'cowplot'

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘testthat’
Running ‘test_package.R’ [0s/1s]
Running the tests in ‘tests/test_package.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘testthat’
Found the following files/directories:
  ‘flux.CH4.txt’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘kableExtra’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

Packages suggested but not available for checking: 'bruceR', 'text'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package required but not available: ‘lubridate’

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggparty', 'ggplot2', 'cowplot', 'testthat'

Packages suggested but not available for checking:
  'caret', 'furrr', 'mlr3verse', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'ggpolypath', 'inlabru', 'testthat', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'solitude', 'C50', 'FactoMineR', 'dplyr', 'factoextra',
  'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running examples in ‘FMM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotFMM
> ### Title: Plot fitted FMM models
> ### Aliases: plotFMM
> 
> ### ** Examples
> 
> 
> # Simulates an scenario in which an FMM model is suitable,
> res <- generateFMM(2,3,1.5,2.3,0.1,outvalues = TRUE,sigmaNoise = 0.3, plot=FALSE)
> # then a FMM model is fitted to the data.
> fit <- fitFMM(res$y, lengthAlphaGrid=20,lengthOmegaGrid=12)
> plotFMM(fit)
> 
> # Components plot of FMM Model fitted to neuronal data with various optional aesthetics
> data("neuronalSpike")
> fittedFMM2<-fitFMM(neuronalSpike, nback=2,
+                    lengthAlphaGrid = 24,lengthOmegaGrid = 10, numReps = 1)
|--------------------------------------------------|
|==================================================|
 Stopped by reaching maximum iterations (2 iteration(s)) 
> 
> plotFMM(fittedFMM2, components = TRUE)
> plotFMM(fittedFMM2, components = TRUE,
+         legendInComponentsPlot = FALSE,
+         textExtra = "Neuronal Data")
> 
> # With ggplot2, customizable plots can be created,
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) FMP.Rd:30: Lost braces; missing escapes or markup?
    30 | \eqn{m(\theta) = b_0 + b_1 \theta + b_2 \theta^2 + b_3 \theta^3}. Acceptable values of k = {0,1,2,3}. According to 
       |                                                                                            ^
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'fda'
Running ‘run_fMRItools_tests.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/run_fMRItools_tests.R’ failed.
Complete output:
  > # Build --> Install and Restart
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘Epi’
checkRd: (-1) Estable.Rd:40: Lost braces
    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
checkRd: (-1) Estable.Rd:41: Lost braces
    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
checkRd: (-1) Estable.Rd:42: Lost braces
    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
checkRd: (-1) Estable.Rd:43-56: Lost braces
    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
checkRd: (-1) FMstable.Rd:51: Lost braces
    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
checkRd: (-1) FMstable.Rd:52: Lost braces
    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
Package required but not available: ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'mixtools'
Running examples in ‘fmx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MaP
> ### Title: Maximum a Posteriori clustering
> ### Aliases: MaP
> 
> ### ** Examples
> 
> x = rnorm(1e2L, sd = 2)
> m = fmx('norm', mean = c(-1.5, 1.5), w = c(1, 2))
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httr2', 'rvest', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(folders)
  > 
  > testthat::test_check("folders")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: ‘shiny.semantic’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'cowplot', 'stringr', 'tibble', 'tidyr',
  'viridis', 'igraph', 'ggraph'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'rstan', 'arm', 'reshape2', 'ggplot2', 'bayesplot', 'dplyr',
  'tidyverse'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'dplyr', 'stringr', 'reshape2', 'ggplot2', 'ggplotify',
  'rvest', 'ggnewscale', 'patchwork'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'lubridate', 'stringr', 'keras', 'echarts4r',
  'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'thief', 'ggplot2', 'purrr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'lubridate', 'ggplot2', 'purrr', 'dtplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'decomposedPSF', 'ggplot2', 'imputeTestbench', 'reshape2', 'forecast'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'mispitools', 'dplyr', 'tidyr', 'fbnet', 'hrbrthemes',
  'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'progress', 'SoilHyP'

Package suggested but not available for checking: ‘testthat’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'stringr', 'dplyr', 'tidyr', 'purrr', 'ggridges',
  'snakecase', 'tibble', 'yardstick', 'forcats', 'patchwork'

Package suggested but not available for checking: ‘testthat’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'tidyr', 'broom', 'purrr', 'tibble',
  'systemfit', 'ggpmisc', 'car', 'FinCal', 'ggdendro'

Package suggested but not available for checking: ‘tidyselect’

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

Package suggested but not available for checking: ‘labelled’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gridtext', 'vdiffr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'Gmisc', 'Greg', 'purrr', 'rms', 'testthat', 'tibble',
  'tidyr', 'tidyselect', 'tidyverse'
Running examples in ‘forestplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: forestplot
> ### Title: Draws a forest plot
> ### Aliases: forestplot forestplot.default forestplot.data.frame
> ###   print.gforge_forestplot plot.gforge_forestplot forestplot.grouped_df
> 
> ### ** Examples
> 
> #############################################
> # Simple examples of how to do a forestplot #
> #############################################
> 
> ask <- par(ask = TRUE)
> 
> # A basic example, create some fake data
> row_names <- list(list("test = 1", expression(test >= 2)))
> test_data <- data.frame(
+   coef = c(1.59, 1.24),
+   low = c(1.4, 0.78),
+   high = c(1.8, 1.55)
+ )
> test_data |>
+   forestplot(labeltext = row_names,
+              mean = coef,
+              lower = low,
+              upper = high,
+              zero = 1,
+              cex  = 2,
+              lineheight = "auto",
+              xlab = "Lab axis txt") |>
+   fp_add_header("Group") |>
+   fp_set_style(lines = gpar(col = "darkblue"))
Error: The package dplyr is needed for this function to work. Please install it.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘forestplot.Rmd’ using rmarkdown

Quitting from lines 53-55 [unnamed-chunk-2] (forestplot.Rmd)
Error: processing vignette 'forestplot.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘forestplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'igraph', 'ggplot2', 'rapportools'

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

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'gt', 'huxtable', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'onbrand', 'readr', 'readxl',
  'stringr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > testthat::test_check("formulaic")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘meta’
Packages suggested but not available for checking:
  'ggplot2', 'ibdsim2', 'testthat'
Running examples in ‘forrel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MPPsims
> ### Title: Missing person power simulations
> ### Aliases: MPPsims
> 
> ### ** Examples
> 
> x = nuclearPed(fa = "Gf", mo = "Gm", children = c("Uncle", "Mother"), sex = 1:2)
> x = addChildren(x, fa = "Father", mo = "Mother", nch = 3, sex = c(1,2,1),
+                 id = c("S1", "S2", "MP"))
Creating new father: Father
> x = addSon(x, "Father", id = "HS")
Creating new mother: 1
> 
> # Brother S1 is already genotyped with a marker with 4 alleles
> x = addMarker(x, S1 = "1/2", alleles = 1:4)
> 
> # Alternatives for additional genotyping
> sel = list("Father", "S2", "HS", c("Gm", "Uncle"))
> 
> plot(x, marker = 1, hatched = sel)
Warning: Alignment failed; switching to simple DAG alignment
> 
> # Simulate
> simData = MPPsims(x, selections = sel, nProfiles = 2, lrSims = 2)
Selection: Baseline
Selection: Father
Selection: S2
Selection: HS
Selection: Gm, Uncle
Total time used: 0.826 secs
> 
> # Power plot
> powerPlot(simData, type = 3)
Error: This function needs the `ggplot2` package, which does not seem to be available. Please install `ggplot2` and try again.
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Hmisc', 'ggplot2', 'tibble'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Distance', 'plotly', 'progress', 'tidyr', 'VoxR', 'vroom'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'FactoMineR', 'forcats', 'ggplot2', 'likert', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown

Quitting from lines 25-33 [unnamed-chunk-1] (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Overview.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FossilSim
> ### Title: FossilSim: A package for simulating and plotting fossil and
> ###   taxonomy data
> ### Aliases: FossilSim FossilSim-package
> 
> ### ** Examples
> 
> # simulate a tree using TreeSim conditioned on tip number
> t = TreeSim::sim.bd.taxa(n = 10, numbsim = 1, lambda = 1, mu = 0.2)[[1]]
Error in loadNamespace(x) : there is no package called ‘TreeSim’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘TreeSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("foto")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: ‘arrow’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) FGf.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FourgameteP.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'purrr', 'ggplot2', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fourierin_details.Rmd’ using rmarkdown

Quitting from lines 50-83 [unnamed-chunk-1] (fourierin_details.Rmd)
Error: processing vignette 'fourierin_details.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘fourierin_details.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'testthat', 'gamm4', 'stringr'

Package suggested but not available for checking: ‘refund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'klaR', 'GGally', 'ggplot2', 'ggeasy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot_lines.Rd:66: Lost braces
    66 | moderator. By default it is equal to \8code{c(19, 17, 15, 8, 5, 4, 3, 1)}.}
       |                                            ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
checkRd: (-1) Fpop.Rd:9: Lost braces; missing escapes or markup?
     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
Package required but not available: ‘fAssets’

Packages suggested but not available for checking: 'parma', 'dplR', 'bcp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'expsmooth', 'fma', 'forecast', 'ggplot2', 'purrr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fable', 'fabletools', 'feasts', 'ggplot2', 'lubridate',
  'purrr', 'tibble', 'tidyr', 'tsibble', 'tsibbledata'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘forecast’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘RandomFields’
Packages suggested but not available for checking: 'ggplot2', 'crqa'
Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'dplyr'
'LazyData' is specified without a 'data' directory
Running examples in ‘fractional-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: numerical
> ### Title: Convert a fractional object to the equivalent numeric object
> ### Aliases: numerical numerical.charFrac numerical.default
> ###   numerical.fractional
> 
> ### ** Examples
> 
> suppressPackageStartupMessages(library(dplyr))
Error in library(dplyr) : there is no package called ‘dplyr’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Theory.Rmd’ using rmarkdown

Quitting from lines 18-26 [c0] (Theory.Rmd)
Error: processing vignette 'Theory.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Theory.Rmd’

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

Quitting from lines 45-48 [c2] (Vulgar_Fractions_in_R.Rmd)
Error: processing vignette 'Vulgar_Fractions_in_R.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Vulgar_Fractions_in_R.Rmd’

SUMMARY: processing the following files failed:
  ‘Theory.Rmd’ ‘Vulgar_Fractions_in_R.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘netmeta’

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

Packages suggested but not available for checking: 'dplyr', 'plotly', 'egg'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Problems with news in ‘NEWS.md’:
No news entries found.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'stringr', 'tidyselect', 'purrr', 'janitor', 'lubridate',
  'tibble', 'forcats', 'rio', 'readr', 'vroom', 'fastDummies'

Packages suggested but not available for checking: 'badger', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) summary.frbs.Rd:32: Lost braces
    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
checkRd: (-1) summary.frbs.Rd:60: Lost braces; missing escapes or markup?
    60 |          {4.0, 0.23, 0.43, 0.53, 0.73} on its column. It means that the label a.2 of variable v.1 
       |          ^
Packages required but not available: 'fdadensity', 'fdapace'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) grade.Rd:57: Lost braces
    57 |   \code{freealg} object comprising terms of grade code{n}.
       |                                                       ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘reshape2’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘frenchCurve-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.data.frame.curve
> ### Title: Conversion to data frame
> ### Aliases: as.data.frame.curve
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘FCEmulator.Rmd’ using rmarkdown

Quitting from lines 13-22 [setup] (FCEmulator.Rmd)
Error: processing vignette 'FCEmulator.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘FCEmulator.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'tibble', 'dplyr', 'tidyr', 'rvest', 'stringr', 'purrr', 'readr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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 suggested but not available for checking: 'fda', 'testthat'
Packages required but not available: 'ggplot2', 'GGally'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'stringr', 'reshape2', 'ggplot2'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  + 	library(testthat)
  + 	library(frequencyConnectedness)
  + 	test_check("frequencyConnectedness")
  + }
  Error in packageVersion("testthat") : 
    there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

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

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'mRMRe', 'epiR', 'DescTools', 'survminer', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) maximin.Rd:197: Lost braces
   197 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) adminlte_color.Rd:64: Lost braces; missing escapes or markup?
    64 |  defaults colors in {shinydashboard}.
       |                     ^
checkRd: (-1) adminlte_global.Rd:21: Lost braces; missing escapes or markup?
    21 |  global settings in {shinydashboard}.
       |                     ^
checkRd: (-1) adminlte_sidebar.Rd:61: Lost braces; missing escapes or markup?
    61 |  the sidebar in {shinydashboard}.
       |                 ^
checkRd: (-1) search_vars_adminlte2.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_adminlte2.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs4dash.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs4dash.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) search_vars_bs4dash.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'usethis'
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘FrF2’

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

Packages suggested but not available for checking:
  'FrF2.catlg128', 'DoE.wrapper'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'dplyr', 'testthat'
Running examples in ‘fritools2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: count_groups
> ### Title: Count Observations per Groups
> ### Aliases: count_groups
> 
> ### ** Examples
> 
> count_groups(mtcars, "am", "gear")
  am gear count
1  0    3    15
2  0    4     4
3  1    4     8
4  1    5     5
> RUnit::checkEquals(dplyr::count(mtcars, am, gear),
+                    count_groups(mtcars, "am", "gear"), checkNames = FALSE)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
  Running ‘tinytest.R’ [2s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'devtools', 'dplyr', 'testthat'
Running examples in ‘fritools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: count_groups
> ### Title: Count Observations per Groups
> ### Aliases: count_groups
> 
> ### ** Examples
> 
> count_groups(mtcars, "am", "gear")
  am gear count
1  0    3    15
2  0    4     4
3  1    4     8
4  1    5     5
> RUnit::checkEquals(dplyr::count(mtcars, am, gear),
+                    count_groups(mtcars, "am", "gear"), checkNames = FALSE)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
  Running ‘tinytest.R’ [2s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'Hmisc', 'ggpubr', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright 2016 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of fromo.
  > #
  > # fromo is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU Lesser General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # fromo is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU Lesser General Public License for more details.
  > #
  > # You should have received a copy of the GNU Lesser General Public License
  > # along with fromo.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2016.03.25
  > # Copyright: Steven E. Pav, 2016-2016
  > # Author: Steven E. Pav
  > # Comments: Steven E. Pav
  > 
  > # because Hadley says it should be like this.
  > # see https://github.com/hadley/devtools/wiki/Testing
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'fishmethods', 'FSA', 'pkgdown', 'readxl'
Package required but not available: ‘car’

Packages suggested but not available for checking:
  'DescTools', 'dplyr', 'fishmethods', 'marked', 'pkgdown', 'testthat',
  'tibble'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'roxygen2', 'stringr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Script needed to run testthat automatically from ‘R CMD check’. See
  > # testthat::test_dir documentation.
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘caret’

Packages suggested but not available for checking:
  'arm', 'C50', 'car', 'Cubist', 'extraTrees', 'foba', 'Hmisc', 'kknn',
  'klaR', 'nodeHarvest', 'obliqueRF', 'penalizedLDA', 'relaxo', 'rrlda'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) FSelector-package.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:22: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘testthat’

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'RTCGA.rnaseq', 'ggplot2', 'tibble', 'pkgdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) report.Rd:18: Lost braces; missing escapes or markup?
    18 |         \item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
Packages required but not available: 'caret', 'dplyr', 'tidyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available:
  'purrr', 'dplyr', 'tibble', 'tidyr', 'readxl', 'readtext'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'pillar', 'testthat', 'tibble', 'vctrs'
GNU make is a SystemRequirements.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'reshape2', 'ggplot2'

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

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

Packages suggested but not available for checking:
  'plotly', 'network', 'ggnetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available:
  'dplyr', 'furrr', 'ggplot2', 'purrr', 'stringr', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
File ‘fstcore/libs/fstcore.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > # required packages
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > # required packages
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'forecast', 'rainbow', 'sde', 'fda', 'fdapace'

Packages suggested but not available for checking:
  'fds', 'R2jags', 'meboot'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplyr’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lme4', 'afex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'igraph', 'devtools', 'ggrepel', 'randomcoloR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'fda', 'ggplot2', 'tidyr', 'patchwork', 'roahd', 'dplyr', 'stringr',
  'fda.usc', 'rofanova'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'DescTools', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'keras', 'tensorflow', 'fda.usc', 'fda', 'ggplot2', 'ggpubr',
  'caret', 'reshape2'

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

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:
  'dplyr', 'tidyr', 'stringr', 'purrr', 'tibble', 'tidyselect'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'fda', 'ggplot2', 'reshape2', 'testthat'
Running examples in ‘funData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.funData
> ### Title: Visualize functional data objects using ggplot
> ### Aliases: autoplot.funData autolayer.funData
> 
> ### ** Examples
> 
> # Install / load package ggplot2 before running the examples
> library("ggplot2")
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘fda’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'fda', 'ggplot2', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggforce', 'ggplot2', 'patchwork', 'purrr',
  'stringr', 'tibble', 'tidyr'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'broom', 'purrr', 'tidyr', 'forcats'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'purrr', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tidytext'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘funrar.Rmd’ using rmarkdown

Quitting from lines 302-362 [unnamed-chunk-8] (funrar.Rmd)
Error: processing vignette 'funrar.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘funrar.Rmd’

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

Quitting from lines 133-141 [unnamed-chunk-3] (new_distinctiveness.Rmd)
Error: processing vignette 'new_distinctiveness.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘new_distinctiveness.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘funrar.Rmd’ ‘new_distinctiveness.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'phytools', 'viridis'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘igraph’

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

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

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

Packages suggested but not available for checking:
  'covid19us', 'Ecdat', 'ggplot2', 'patchwork', 'randomcoloR',
  'readxl', 'reshape2'

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

Package suggested but not available for checking: ‘testthat’

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'attachment', 'devtools', 'lightparser', 'roxygen2', 'tibble',
  'tidyr', 'usethis'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘subgroup_fusion.Rmd’ using rmarkdown

Quitting from lines 64-76 [unnamed-chunk-2] (subgroup_fusion.Rmd)
Error: processing vignette 'subgroup_fusion.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘subgroup_fusion.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘FusionLearn.Rmd’ using rmarkdown

Quitting from lines 37-45 [unnamed-chunk-1] (FusionLearn.Rmd)
Error: processing vignette 'FusionLearn.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘FusionLearn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
Package required but not available: ‘batchtools’

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

Package suggested but not available for checking: ‘future.batchtools’

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) genmf.Rd:26: Lost braces; missing escapes or markup?
    26 | \item 'gbellmf' is c(\code{a, b, c}), where \code{a} denotes the width, \code{b} is usually positive and {c} locates the center of the curve.
       |                                                                                                          ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘markovchain’
Packages suggested but not available for checking: 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following HTML validation problems:
FuzzyNumberList.html:76:1 (FuzzyNumberList.Rd:285): Warning: trimming empty <ul>
TrapezoidalFuzzyNumberList.html:118:1 (TrapezoidalFuzzyNumberList.Rd:572): Warning: trimming empty <ul>
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘car’

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

Packages suggested but not available for checking: 'progress', 'styler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'egg', 'ggforce', 'ggplot2', 'ggrepel', 'ggplotify',
  'ggpubr', 'tidyr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplyr’
Running examples in ‘gadget3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: likelihood_catchdistribution
> ### Title: Gadget3 likelihood actions
> ### Aliases: g3l_distribution_sumofsquares g3l_distribution_multinomial
> ###   g3l_distribution_multivariate g3l_distribution_surveyindices_log
> ###   g3l_distribution_surveyindices_linear
> ###   g3l_distribution_sumofsquaredlogratios g3_distribution_preview
> ###   g3l_abundancedistribution g3l_catchdistribution
> 
> ### ** Examples
> 
> ## Don't show: 
> library(magrittr)
> ## End(Don't show)
> ling_imm <- g3_stock('ling_imm', seq(20, 156, 4)) %>% g3s_age(3, 10)
> ling_mat <- g3_stock('ling_mat', seq(20, 156, 4)) %>% g3s_age(5, 15)
> lln <- g3_fleet('lln')
> 
> # Invent a ldist.lln table for our tests
> ldist.lln.raw <- data.frame(
+     year = c(1999, 2000),
+     age = sample(5:9, 100, replace = TRUE),
+     length = sample(10:70, 100, replace = TRUE),
+     number = 1,
+     stringsAsFactors = FALSE)
> 
> # Group length into 10-long bins
> # NB: The last 2 bins will be empty, but gadget3 will use the factor levels, include them as zero
> # NB: Generally one would use mfdb::mfdb_sample_count() source and group data for you
> ldist.lln.raw |> dplyr::group_by(
+   year = year, age = age,
+   length = cut(length, breaks = seq(10, 100, by = 10), right = FALSE)
+ ) |> dplyr::summarise(number = sum(number), .groups = 'keep') -> ldist.lln
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘incorporating-observation-data.Rmd’ using rmarkdown

Quitting from lines 26-29 [unnamed-chunk-2] (incorporating-observation-data.Rmd)
Error: processing vignette 'incorporating-observation-data.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘incorporating-observation-data.Rmd’

--- re-building ‘introduction-single-stock.Rmd’ using rmarkdown

Quitting from lines 101-103 [unnamed-chunk-6] (introduction-single-stock.Rmd)
Error: processing vignette 'introduction-single-stock.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘introduction-single-stock.Rmd’

--- re-building ‘model-customisation.Rmd’ using rmarkdown
--- finished re-building ‘model-customisation.Rmd’

--- re-building ‘model-debugging.Rmd’ using rmarkdown
--- finished re-building ‘model-debugging.Rmd’

--- re-building ‘model-structure.Rmd’ using rmarkdown
--- finished re-building ‘model-structure.Rmd’

--- re-building ‘multiple-substocks.Rmd’ using rmarkdown

Quitting from lines 58-73 [unnamed-chunk-4] (multiple-substocks.Rmd)
Error: processing vignette 'multiple-substocks.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘multiple-substocks.Rmd’

--- re-building ‘random-effects.Rmd’ using rmarkdown

Quitting from lines 59-74 [unnamed-chunk-4] (random-effects.Rmd)
Error: processing vignette 'random-effects.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘random-effects.Rmd’

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

SUMMARY: processing the following files failed:
  ‘incorporating-observation-data.Rmd’ ‘introduction-single-stock.Rmd’
  ‘multiple-substocks.Rmd’ ‘random-effects.Rmd’

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'httr2', 'potions', 'purrr', 'readr', 'stringr', 'tibble',
  'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'gt', 'kableExtra', 'pkgdown', 'testthat'

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

Packages suggested but not available for checking:
  'gamm4', 'PLmixed', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'purrr', 'tibble', 'ryandexdirect',
  'rfacebookstat', 'rvkstat', 'rmytarget', 'rym', 'rgoogleads',
  'rappsflyer'

Package suggested but not available for checking: ‘testthat’

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'traits', 'dplyr', 'ggplot2', 'heatmaply', 'reshape2', 'dendextend'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'hrbrthemes', 'gganimate', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) stabsel.mboostLSS.Rd:44: Lost braces
    44 |     always use code{"none"}.}
       |                    ^
Package suggested but not available for checking: ‘car’
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gameR.Rmd’ using rmarkdown

Quitting from lines 20-25 [setup] (gameR.Rmd)
Error: processing vignette 'gameR.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘gameR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) naref.Rd:13: Lost braces
    13 | \details{ For every \code{factor} or \code{character} column in \code{x}, \code{naref} sets \code{NA} as the reference level for a \code{factor} variable. Columns coded as \code{character} class are first converted to factors via \R{factor(x)}.  If \code{impute=TRUE} then the numeric columns are converted to two columns, one appended \code{.x} that contains imputed values and another appended \code{.miss} which is a binary variable indicating whether the original value was missing.  Numeric columns are returned without change if \code{impute=FALSE} or if they do not contain any missing values.  
       |                                                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘distributions3’
checkRd: (-1) pc.Rd:17: Lost braces
    17 | The functions \code{gamlss.pcr()} and \code{gamlss.pc()} are supporting functions. The  are not intended to be called directly by users. The function \code{gamlss.pc()} is using the linear model function \code{lm()} to fit the first principal components while the function code{gamlss.pcr()} uses \code{fitPCR()}.
       |                                                                                                                                                                                                                                                                                      ^
Packages required but not available: 'ggridges', 'ggplot2'

Packages suggested but not available for checking:
  'reshape2', 'igraph', 'networkD3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) term.plotZadj.Rd:6: Lost braces
     6 |  \ This is a wrapper to function \code{\link[gamlss]{term.plot}}. code{term.plotZadj} produces term plots for a specified parameter from a    
       |                                                                       ^
Package suggested but not available for checking: ‘distributions3’
Package required but not available: ‘lme4’

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

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

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

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: ‘Ecdat’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #
  > # GAMS - General Algebraic Modeling System R API
  > #
  > # Copyright (c) 2017-2024 GAMS Software GmbH <support@gams.com>
  > # Copyright (c) 2017-2024 GAMS Development Corp. <support@gams.com>
  > #
  > # Permission is hereby granted, free of charge, to any person obtaining a copy
  > # of this software and associated documentation files (the "Software"), to deal
  > # in the Software without restriction, including without limitation the rights
  > # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  > # copies of the Software, and to permit persons to whom the Software is
  > # furnished to do so, subject to the following conditions:
  > #
  > # The above copyright notice and this permission notice shall be included in all
  > # copies or substantial portions of the Software.
  > #
  > # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  > # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  > # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  > # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  > # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  > # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  > # SOFTWARE.
  > #
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tensorflow’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'tidyr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

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

Packages suggested but not available for checking:
  'BradleyTerry2', 'DiagrammeR', 'R2jags', 'cowplot', 'haplo.stats',
  'manhattanly', 'meta', 'pedigreemm', 'readr', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) glag.Rd:7: Lost braces; missing escapes or markup?
     7 | Similar to the \code{\link{lag}} function from the \code{stats} package, but \code{glag} enables padding (e.g. {NA}s or 0s) of the lost entries. Contrary to the \code{\link{lag}} function in the stats package, however, the default in \code{glag} is to pad (with \code{NA}s). The \code{glag} is particularly suited for \code{\link{zoo}} objects, since their indexing is retained
       |                                                                                                                ^
Package required but not available: ‘vcfR’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'forecast', 'ggplot2', 'lubridate', 'nloptr', 'tswge'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                      ^
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                                      ^
checkRd: (-1) read.ctable.Rd:29: Lost braces; missing escapes or markup?
    29 | output array, {row,col}.names are not necessary \code{dimnames[[1]]} and
       |               ^
Packages required but not available: 'tibble', 'vctrs'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'nloptr', 'tidyr'

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

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

Packages suggested but not available for checking: 'kableExtra', 'rvest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tibble', 'ggplot2', 'rstan', 'stringr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'rgbif', 'CoordinateCleaner', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'ggrepel', 'tidyr'
Running examples in ‘GauPro-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cubic
> ### Title: Cubic Kernel R6 class
> ### Aliases: Cubic k_Cubic
> 
> ### ** Examples
> 
> k1 <- Cubic$new(beta=runif(6)-.5)
> plot(k1)
Error in loadNamespace(x) : there is no package called ‘ggplot2’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) Sim.Markov.Chain.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{eta0}{inital value in {1,...,r}.}
       |                             ^
Packages required but not available: 'ggplot2', 'metR'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CompoundDensPlot.Rd:18: Lost braces
    18 |   \item{shape1, scale ,shape2, shape3}{numeric; positive parameters of the GB2 distribution. On the plot they are denotes as \code{a}, code{b}, \code{p}, \code{q} and \code{pl0} respectively.}
       |                                                                                                                                            ^
checkRd: (-1) CompoundVarest.Rd:58: Lost braces
    58 | \code{scoreU.cgb2} returns a \eqn{N \times (L-1)} matrix of scores <code{U}.
       |                                                                         ^
checkRd: (-1) Fisk.Rd:26: Lost braces
    26 | \value{\code{fisk} and \code{fiskh} return vectors of length 4 containing the estimated parameters \eqn{a}, eqn{b}, as well as \eqn{p=1} and \eqn{q=1}. 
       |                                                                                                                ^
checkRd: (-1) MLfullGB2.Rd:23: Lost braces
    23 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
checkRd: (-1) MLprofGB2.Rd:16: Lost braces
    16 |   \item{method}{numeric; the method to be used by \code{optim}. By default, code{method = }1 and the used method is BFGS. If \code{method = }2, method L-BFGS-B is used.}
       |                                                                                 ^
Packages required but not available:
  'devtools', 'tidyverse', 'stringr', 'tibble', 'caret'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'beepr', 'dplyr', 'ggmap', 'ggplot2', 'ggspatial', 'lubridate',
  'readr', 'tidyselect', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pdp', 'vip', 'viridis'
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘gputools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘paleofire’
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) listInverseBlocks.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                           ^
checkRd: (-1) listInverseBlocks.Rd:17: Lost braces; missing escapes or markup?
    17 | List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                    ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gconsensus.Rd:48-54: Lost braces
    48 | {\code{display.signif.digits} an integer representing the number of significant digits to be obtained in the adaptative approach of the Monte Carlo simulation,
       | ^
Package required but not available: ‘postpack’

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

Packages suggested but not available for checking:
  'caret', 'cowplot', 'ggplot2', 'lubridate', 'readxl', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) GCTF.Rd:56: Lost braces; missing escapes or markup?
    56 |   U : A matrix which has N-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:57: Lost braces; missing escapes or markup?
    57 |   V : A matrix which has M-rows and J-columns (J < {N, M}).
       |                                                    ^
checkRd: (-1) GCTF.Rd:58: Lost braces; missing escapes or markup?
    58 |   J : The number of dimension (J < {N, M}).
       |                                    ^
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("gcTensor")
  > library("rTensor")
  > library("einsum")
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'nls.multstart'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘GDAdata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Decathlon
> ### Title: Top performances in the Decathlon from 1985 to 2006.
> ### Aliases: Decathlon
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Decathlon, package="GDAdata")
> summary(Decathlon[, grep("P.*", names(Decathlon))])
   Polevault         P100m             Plj              Psp       
 Min.   :2.850   Min.   : 597.0   Min.   : 569.0   Min.   :418.0  
 1st Qu.:4.200   1st Qu.: 765.0   1st Qu.: 757.0   1st Qu.:622.0  
 Median :4.400   Median : 806.0   Median : 804.0   Median :672.0  
 Mean   :4.405   Mean   : 806.6   Mean   : 807.4   Mean   :674.6  
 3rd Qu.:4.650   3rd Qu.: 847.0   3rd Qu.: 857.0   3rd Qu.:726.0  
 Max.   :5.760   Max.   :1042.0   Max.   :1089.0   Max.   :941.0  
      Phj           P400m         P110h             Ppv              Pdt       
 Min.   : 396   Min.   :532   Min.   : 526.0   Min.   : 321.0   Min.   :231.0  
 1st Qu.: 696   1st Qu.:746   1st Qu.: 777.0   1st Qu.: 673.0   1st Qu.:600.0  
 Median : 749   Median :789   Median : 824.0   Median : 731.0   Median :655.0  
 Mean   : 749   Mean   :788   Mean   : 821.6   Mean   : 734.4   Mean   :657.8  
 3rd Qu.: 803   3rd Qu.:832   3rd Qu.: 868.0   3rd Qu.: 804.0   3rd Qu.:713.0  
 Max.   :1061   Max.   :998   Max.   :1044.0   Max.   :1152.0   Max.   :970.0  
      Pjt             P1500      
 Min.   : 330.0   Min.   :121.0  
 1st Qu.: 588.0   1st Qu.:607.0  
 Median : 644.0   Median :669.0  
 Mean   : 648.1   Mean   :661.7  
 3rd Qu.: 707.0   3rd Qu.:725.0  
 Max.   :1040.0   Max.   :946.0  
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package suggested but not available for checking: ‘lubridate’
Packages suggested but not available for checking: 'gt', 'testthat'
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) nearblack.Rd:30: Lost braces
    30 | code{infile=}, indicating that the input file should be
       |     ^
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) is.what.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) is.what.Rd:25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) is.what.Rd:26-27: Lost braces in \enumerate; meant \describe ?
Packages required but not available:
  'descriptio', 'FactoMineR', 'ggplot2', 'ggrepel'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'RSQLite', 'dplyr', 'stringr', 'readr', 'progress'

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: ‘testthat’
Packages required but not available:
  'dplyr', 'ggplot2', 'progress', 'tibble'

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

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

Packages suggested but not available for checking:
  'cdmTools', 'testthat', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httr2’

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: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'purrr', 'stringr', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) GDSARM.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDSARM.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) GDS_givencols.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDS_givencols.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) dantzig.delta.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dantzigS.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dataCompoundExt.Rd:6: Lost braces
     6 | \title{Compound Extraction experiment of Dopico-Garc{\' i}a et al. (2007)}
       |                                                     ^
checkRd: (-1) dataCompoundExt.Rd:35: Lost braces
    35 | An analytical experiment conducted by Dopico-Garc{\' i}a et al. (2007) to
       |                                                  ^
checkRd: (-1) dataCompoundExt.Rd:22: Lost braces
    22 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'gdxrrw', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'autoimage', 'optimx'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'red', 'biomod2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geepack', 'ggplot2', 'lme4', 'MESS'

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) dental.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:21: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘lme4’

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

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

Package suggested but not available for checking: ‘TreeSim’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gelnet.logreg.obj.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
Packages suggested but not available for checking: 'testthat', 'readr'
'LazyData' is specified without a 'data' directory
Running examples in ‘gemma2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calc_XHiY
> ### Title: Calculate XHiY
> ### Aliases: calc_XHiY
> 
> ### ** Examples
> 
> readr::read_tsv(system.file("extdata",
+ "mouse100.pheno.txt",
+ package = "gemma2"),
+ col_names = FALSE) -> pheno
Error in loadNamespace(x) : there is no package called ‘readr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘compare-with-GEMMAv096.Rmd’ using rmarkdown

Quitting from lines 74-78 [unnamed-chunk-1] (compare-with-GEMMAv096.Rmd)
Error: processing vignette 'compare-with-GEMMAv096.Rmd' failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘compare-with-GEMMAv096.Rmd’

SUMMARY: processing the following file failed:
  ‘compare-with-GEMMAv096.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'igraph', 'meta', 'forcats'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggnetwork', 'ggplot2', 'ggraph', 'igraph', 'network', 'phangorn',
  'reshape2', 'ggtree', 'dplyr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GeneF-internal.Rd:40: Lost braces; missing escapes or markup?
    40 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.pvalue.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
Packages required but not available:
  'ggplot2', 'ggpubr', 'reshape2', 'stringr', 'tibble', 'tidyr', 'vcfR'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clusterProfiler', 'dplyr', 'europepmc', 'geneset', 'ggplot2',
  'ggraph', 'ggvenn', 'igraph', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'AnnotationDbi', 'cowplot', 'ComplexUpset', 'forcats', 'fgsea',
  'ggplotify', 'ggsci', 'ggrepel', 'ggridges', 'ggnewscale', 'GOplot',
  'GOSemSim', 'treemap', 'reshape2', 'rio', 'rrvgo', 'testthat'

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

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

Packages suggested but not available for checking:
  'fgsea', 'dplyr', 'msigdbr'

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mlogit’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'DataVisualizations', 'reshape2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Problems with news in ‘NEWS.md’:
No news entries found.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'reshape2', 'testthat', 'tibble',
  'tidyr', 'tmod'

Packages suggested but not available for checking:
  'clusterProfiler', 'GO.db', 'UpSetR', 'AnnotationHub', 'ensembldb',
  'org.Hs.eg.db'

Package which this enhances but not available for checking: ‘simplifyEnrichment’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'httr2', 'dplyr', 'readr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GGEBiplots', 'ggforce', 'ggplot2', 'dplyr', 'missMDA', 'reshape2',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) LD.Rd:37-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:47-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:66-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:82-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:48-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:59-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:78-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:97-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available:
  'sfnetworks', 'igraph', 'dplyr', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'dtplyr', 'purrr', 'stringr', 'sunburstR', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'gt', 'gtsummary', 'plotly', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'readr', 'tibble', 'dplyr'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'purrr', 'dplyr', 'tidyr', 'ggplot2', 'tibble', 'forcats', 'readr',
  'rio'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggridges', 'hierfstat', 'stringr', 'tibble', 'vcfR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'reactome.db', 'AnnotationDbi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) barto.Rd:15-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:19-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) barto.Rd:23-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chrY_subseg.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mauve_bbone.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mauve_bbone.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) three_genes.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) three_genes.Rd:19-20: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'cowplot', 'dplyr', 'ggplot2', 'tidyr'

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

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

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

Package suggested but not available for checking: ‘vcdExtra’

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

Package suggested but not available for checking: ‘igraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
checkRd: (-1) cfunc.new.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cfunc.new.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                ^
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                            ^
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'dplyr', 'Hmisc'

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'gt', 'geofacet', 'ggplot2', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'arrow', 'testthat'
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘optimx’

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'furrr', 'ggplot2', 'ggpubr', 'latex2exp', 'purrr', 'tidyr',
  'tidyselect', 'tidyterra'

Packages suggested but not available for checking:
  'elevatr', 'ggthemes', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tmap', 'reldist', 'dplyr', 'reshape2', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘archive’
Packages required but not available:
  'dplyr', 'snakecase', 'tibble', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) calvaria.Rd:8: Lost braces; missing escapes or markup?
     8 | A named list containing \code{x} {a vector containing the ages}
       |                                  ^
checkRd: (-1) calvaria.Rd:9: Lost braces; missing escapes or markup?
     9 |   \code{y} {a matrix where each column is a preshape.} The 23rd, 101st,
       |            ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'ggrepel'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'geofacet', 'httptest', 'janitor', 'patchwork',
  'readr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Packages required but not available:
  'dplyr', 'geomultistar', 'readr', 'rolap', 'stringr', 'tibble',
  'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'dbplyr', 'DiagrammeR', 'dm', 'RSQLite', 'snakecase', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'gistr', 'RPostgres', 'testthat'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: feature
> ### Title: feature class
> ### Aliases: feature
> 
> ### ** Examples
> 
> # point -> feature
> x <- '{ "type": "Point", "coordinates": [100.0, 0.0] }'
> point(x) %>% feature()
<Feature> 
  type:  Point 
  coordinates:  [100.0,0.0] 
> 
> # multipoint -> feature
> x <- '{"type": "MultiPoint", "coordinates": [ [100.0, 0.0], [101.0, 1.0] ] }'
> multipoint(x) %>% feature()
<Feature> 
  type:  MultiPoint 
  coordinates:  [[100.0,0.0],[101.0,1.0]] 
> 
> # linestring -> feature
> x <- '{ "type": "LineString", "coordinates": [ [100.0, 0.0], [101.0, 1.0] ] }'
> linestring(x) %>% feature()
<Feature> 
  type:  LineString 
  coordinates:  [[100.0,0.0],[101.0,1.0]] 
> 
> # multilinestring -> feature
> x <- '{ "type": "MultiLineString",
+  "coordinates": [ [ [100.0, 0.0], [101.0, 1.0] ], [ [102.0, 2.0], [103.0, 3.0] ] ] }'
> multilinestring(x) %>% feature()
<Feature> 
  type:  MultiLineString 
  coordinates:  [[[100.0,0.0],[101.0,1.0]],[[102.0,2.0],[103.0,3.0]]] 
> 
> # add to a data.frame
> library('tibble')
Error in library("tibble") : there is no package called ‘tibble’
Execution halted
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘geojson-operations.Rmd’ using rmarkdown

Quitting from lines 147-149 [unnamed-chunk-16] (geojson-operations.Rmd)
Error: processing vignette 'geojson-operations.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘geojson-operations.Rmd’

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

SUMMARY: processing the following file failed:
  ‘geojson-operations.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
Packages required but not available:
  'censable', 'dataverse', 'dplyr', 'ggplot2', 'readr', 'stringr',
  'tibble', 'tidyr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'geomarocdata'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'forecast', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following HTML validation problems:
extprod3d.html:24:32 (extprod3d.Rd:24): Warning: trimming empty <code>
extprod3d.html:29:32 (extprod3d.Rd:27): Warning: trimming empty <code>
Packages required but not available: 'caret', 'arm', 'Cubist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'RRPP', 'ggplot2'

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DescTools', 'ggplot2', 'dplyr', 'ggrepel'

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

Package suggested but not available for checking: ‘testthat’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.geos_geometry
> ### Title: Plot GEOS geometries
> ### Aliases: plot.geos_geometry
> 
> ### ** Examples
> 
> plot(as_geos_geometry("LINESTRING (0 0, 1 1)"))
Error: Package 'vctrs' is required for plot.geos_geometry()
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'rstan'

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

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

Package which this enhances but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggspatial', 'ggthemes', 'stringr', 'tidyselect',
  'viridis'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tourr', 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘DescTools’

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

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

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

Packages suggested but not available for checking: 'gsheet', 'inti'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘gert/libs/gert.so’:
  Found non-API call to R: ‘R_curErrorBuf’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘libgit2.R’ [0s/1s]
  Comparing ‘libgit2.Rout’ to ‘libgit2.Rout.save’ ...4,6d3
< Linking to libgit2 v1.7.2, ssh support: YES
< Global config: /home/hornik/.gitconfig
< Default user: myname <my@email.com>
  Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'rio', 'stringr'

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

Packages suggested but not available for checking:
  'lubridate', 'patchwork', 'plotly', 'testthat', 'tidyverse'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'dplyr', 'readr', 'lubridate', 'purrr', 'rvest', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'dplyr', 'readr', 'reshape2', 'tibble', 'lubridate'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'devtools'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_getDTeval.Rmd’ using rmarkdown

Quitting from lines 157-166 [example_2] (Introduction_to_getDTeval.Rmd)
Error: processing vignette 'Introduction_to_getDTeval.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Introduction_to_getDTeval.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'stringr', 'dplyr', 'readr', 'lubridate', 'purrr', 'rvest',
  'GetDFPData2'

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

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

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'readxl', 'purrr', 'tibble'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘run-all.R’ [0s/0s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'purrr', 'readr'

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

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

Packages suggested but not available for checking:
  'fda', 'fda.usc', 'patchwork', 'testthat'

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) vargaugeiis.Rd:22: Lost braces
    22 | \details{The function computes the variance of the Gauge (false-positive rate of outliers in impulse indicator saturation) for a given level of significance of selection (\code{t.pval}) and sample size ({\code{T}) based on Jiao and Pretis (2019). This is an auxilliary function used within the \code{\link{outliertest}} function.}}
       |                                                                                                                                                                                                            ^
Packages required but not available:
  'stringr', 'readxl', 'tidyr', 'rvest', 'dplyr', 'humanize', 'purrr',
  'tibble'

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

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

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

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'stringr', 'animation'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RGtk2’
checkRd: (-1) QANOVA.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) QANOVA.Rd:67: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘GFDmcv’

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: 'dplyr', 'TeachingSampling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rvest', 'tidyr', 'scatterpie', 'ggplot2', 'ggrepel',
  'googlesheets4', 'gsheet'

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

Packages suggested but not available for checking:
  'AOV1R', 'car', 'GGally', 'lmerTest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) gfonts.Rd:8: Lost braces; missing escapes or markup?
     8 | Download Google fonts and generate CSS to use in {rmarkdown} documents and
       |                                                  ^
checkRd: (-1) gfonts.Rd:9: Lost braces; missing escapes or markup?
     9 | {shiny} applications. Some popular fonts are included and ready to use.
       | ^
checkRd: (-1) use_pkg_gfont.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use a Google Font included in {gfonts}}
       |                                      ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘mice’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggpubr', 'progress', 'stringr'

Package suggested but not available for checking: ‘Hmisc’

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'babynames', 'ggrepel', 'ggfittext', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'ggstats', 'progress'

Packages suggested but not available for checking:
  'broom', 'broom.helpers', 'ggforce', 'Hmisc', 'igraph', 'intergraph',
  'labelled', 'network', 'sna', 'roxygen2', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tibble', 'plotly'

Packages suggested but not available for checking:
  'testthat', 'ggthemes', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'flexsurv'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'progress', 'transformr', 'tweenr', 'vctrs'

Packages suggested but not available for checking: 'magick', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'purrr', 'tidyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'vctrs'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cartographer', 'dplyr', 'ggmapinset', 'ggplot2', 'tidyr', 'vctrs'

Packages suggested but not available for checking: 'ggrepel', 'nswgeo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'broom', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'hms', 'labelled', 'lubridate',
  'purrr', 'snakecase', 'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'patchwork', 'testthat', 'tibble', 'vdiffr', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'ggnewscale'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggnewscale', 'ggrepel', 'imager', 'patchwork',
  'tibble', 'tidyr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggfun', 'ggplot2', 'ggplotify', 'aplot'

Packages suggested but not available for checking:
  'cowplot', 'ggimage', 'patchwork', 'pillar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'purrr', 'readr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'purrr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'patchwork'

Packages suggested but not available for checking:
  'gapminder', 'tibble', 'tidyr', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'readr', 'egg', 'vctrs', 'tibble',
  'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'gghalves'

Packages suggested but not available for checking: 'viridis', 'MetBrewer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'ggraph', 'ggrepel', 'igraph',
  'pillar', 'purrr', 'stringr', 'tibble', 'tidygraph'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'vctrs', 'tibble'

Packages suggested but not available for checking: 'vdiffr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tibble', 'vctrs', 'distributional'

Packages suggested but not available for checking:
  'tidyselect', 'dplyr', 'fda', 'posterior', 'testthat', 'vdiffr',
  'broom', 'patchwork', 'tidyr', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'roxygen2', 'tibble', 'ggrepel', 'patchwork', 'geomtextpath'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggnewscale'

Packages suggested but not available for checking: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'labelled', 'patchwork', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'purrr', 'tibble', 'colourpicker'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'brms', 'broom', 'car', 'effects', 'gamm4', 'geepack',
  'ggplot2', 'ggrepel', 'glmmTMB', 'gt', 'haven', 'lme4', 'logistf',
  'mice', 'nestedLogit', 'parsnip', 'patchwork', 'rms', 'rstanarm',
  'sdmTMB', 'see', 'testthat', 'tibble', 'vdiffr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'igraph', 'reshape2', 'plotly'

Packages suggested but not available for checking:
  'stringr', 'roxygen2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyverse', 'RSDA', 'dplyr', 'tidyr', 'stringr',
  'ggforce', 'ggpubr', 'ggthemes', 'tibble', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'stringr'

Packages suggested but not available for checking: 'testthat', 'zeitgebr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'colourpicker', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FactoMineR', 'ggiraph', 'ggplot2', 'dplyr', 'forcats', 'purrr',
  'stringr', 'tibble', 'tidyr', 'tidyselect', 'vctrs', 'ggrepel',
  'tabxplor', 'ggforce'

Packages suggested but not available for checking:
  'widgetframe', 'finalfit', 'kableExtra', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'CopernicusMarine', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'tidyr', 'ggridges', 'fishmethods',
  'broom', 'tidyselect', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gridtext', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggh4x'

Packages suggested but not available for checking: 'tinysnapshot', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'igraph', 'ggplot2', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘rcartocolor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tweenr', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'concaveman', 'latex2exp', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggridges', 'mosaicCore', 'tibble', 'stringr', 'labelled'

Packages suggested but not available for checking:
  'tidyr', 'dplyr', 'mosaic', 'testthat', 'vdiffr', 'lubridate',
  'broom', 'purrr', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'forecast', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggfx', 'ggimage', 'ggpp', 'ggtext', 'paletteer',
  'patchwork', 'stringr', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'ggplotify', 'tidyr', 'ggnewscale'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magick', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggfittext'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'animation'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("ggplot2"): there is no package called ‘ggplot2’

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Packages required but not available: 'ggplot2', 'ggrepel'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'aplot', 'factoextra', 'tibble', 'ggpubr', 'tidyr',
  'patchwork'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'ggrepel', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'geomtextpath', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'profvis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'ggthemes', 'patchwork', 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggfun', 'ggplotify', 'magick', 'tibble'

Package suggested but not available for checking: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'stringr', 'tibble'

Package suggested but not available for checking: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ipaddress', 'dplyr', 'tidyr', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggiraph', 'reshape2', 'sjmisc', 'stringr', 'tidyr',
  'purrr', 'dplyr'

Packages suggested but not available for checking:
  'ggforce', 'ztable', 'moonBook', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'purrr', 'vctrs'

Packages suggested but not available for checking: 'dplyr', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'unisensR', 'lubridate', 'ActCR'

Packages suggested but not available for checking: 'testthat', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggridges', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'broom', 'broom.mixed', 'dplyr', 'patchwork', 'purrr',
  'tibble', 'tidyr', 'vctrs'

Packages suggested but not available for checking: 'lme4', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'stringr', 'purrr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'tibble', 'tidyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'GGally'

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'mice', 'purrr', 'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'patchwork', 'plotly', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'GGally', 'ggplot2', 'network', 'sna'

Packages suggested but not available for checking:
  'car', 'dplyr', 'NetworkToolbox', 'NetworkComparisonTest', 'nlshrink'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GGally', 'network', 'sna', 'ggplot2', 'GGMncv'

Package suggested but not available for checking: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'productplots', 'dplyr', 'plotly', 'purrr', 'tidyr',
  'ggrepel'

Package suggested but not available for checking: ‘patchwork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘network’
Running examples in ‘GGMselect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: selectFast
> ### Title: Estimate a graph in a Gaussian Graphical Model: Fast procedure
> ### Aliases: selectFast
> ### Keywords: multivariate graphs models
> 
> ### ** Examples
> 
> p=30
> n=30
> # simulate graph
> eta=0.11
> Gr <- simulateGraph(p,eta)
> # simulate data
> X <- rmvnorm(n, mean=rep(0,p), sigma=Gr$C)
> # estimate graph
> GRest <- selectFast(X, family="C01")
> 
> # plot result
> library(network)
Error in library(network) : there is no package called ‘network’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Notice.Rnw’ using Sweave
Loading required package: mvtnorm

Error: processing vignette 'Notice.Rnw' failed with diagnostics:
 chunk 2 
Error in library(network) : there is no package called ‘network’

--- failed re-building ‘Notice.Rnw’

SUMMARY: processing the following file failed:
  ‘Notice.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'stringr', 'tibble', 'testthat', 'tidyverse', 'nycflights13'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggrepel', 'network', 'igraph', 'sna'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'ggspatial', 'cowplot', 'ggnewscale'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'ggraph', 'igraph', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggforce', 'tidyr', 'ggplot2', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'stringr', 'tidytext'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'AER', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'magick'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'vctrs'

Packages suggested but not available for checking:
  'dplyr', 'gganimate', 'magick', 'readr', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tibble', 'tidyselect', 'tidyr'

Packages suggested but not available for checking:
  'purrr', 'testthat', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'aplot', 'DESeq2', 'dplyr', 'GGally', 'ggplot2', 'ggh4x', 'lefser',
  'Maaslin2', 'MicrobiomeStat', 'readr', 'tibble', 'tidyr', 'ggprism',
  'patchwork'

Package suggested but not available for checking: ‘ggplotify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'ggnewscale', 'ggplot2', 'ggrepel', 'stringr'

Package suggested but not available for checking: ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'stringr', 'tidyr', 'forcats'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'vctrs'

Packages suggested but not available for checking:
  'dplyr', 'Hmisc', 'profvis', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'EnvStats', 'ggpp', 'ggstats'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tibble', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'tidyverse', 'ggplot2', 'dplyr', 'tibble', 'ggthemes',
  'moonBook', 'editData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'ggplot2', 'stringr', 'readr', 'haven', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'aplot', 'cowplot', 'ggimage'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpp', 'ggplot2', 'tibble', 'dplyr', 'lubridate'

Packages suggested but not available for checking:
  'ggrepel', 'broom', 'broom.mixed', 'gginnards', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggforce', 'stringr', 'GGally', 'tidyr', 'dplyr', 'purrr',
  'readr'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'rxode2', 'nlmixr2', 'lixoftConnectors', 'xgxr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'viridis', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'ggtext', 'ggrepel', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'ezcox', 'ggnewscale'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'vctrs', 'tibble', 'dplyr', 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'ggrepel', 'gginnards', 'magick', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggbeeswarm', 'ggnewscale', 'patchwork', 'rstatix', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggrepel', 'ggsci', 'tidyr', 'purrr', 'dplyr', 'cowplot',
  'ggsignif', 'rstatix', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourpicker', 'dplyr', 'GGally', 'ggbeeswarm', 'ggh4x', 'ggplot2',
  'ggpmisc', 'ggrepel', 'ggpubr', 'ggstance', 'Hmisc', 'plotly',
  'stringr', 'survminer', 'tidyr', 'shinyFiles', 'RPostgres',
  'forcats', 'ggridges', 'rms', 'tibble', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'pkgdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'vctrs'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'gghalves', 'ggpp', 'vctrs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'randomForestSRC', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'ggforce', 'igraph', 'ggrepel', 'viridis',
  'tidygraph', 'graphlayouts', 'vctrs'

Packages suggested but not available for checking:
  'network', 'purrr', 'tibble', 'gganimate', 'sfnetworks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'mixtools', 'bgmm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggbeeswarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'ggplot2', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘redist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'ggpp', 'patchwork', 'devtools', 'ggbeeswarm',
  'dplyr', 'readr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'ggplot2', 'plotly', 'qqplotr', 'stringr'

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'lme4', 'lmerTest', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRbase', 'CVglasso'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'patchwork', 'forcats', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'egg', 'do', 'set', 'cutoff', 'rms', 'nomogramFormula',
  'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'stringr', 'ggplot2', 'tibble', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'stringr', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'ggpubr', 'ggridges', 'viridis', 'hrbrthemes',
  'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'Seurat', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'plotly', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'vctrs'

Packages suggested but not available for checking:
  'vdiffr', 'devtools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'forcats', 'ggh4x', 'ggrepel', 'ggtext', 'haven',
  'patchwork', 'purrr', 'tidyr', 'usethis'

Packages suggested but not available for checking:
  'ggthemes', 'hrbrthemes', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'vctrs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tibble', 'vctrs'

Packages suggested but not available for checking:
  'tidyr', 'dplyr', 'testthat', 'vdiffr', 'ggdendro', 'viridis',
  'waldo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking: 'ggmap', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'tibble'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'tinysnapshot', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'rosm', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggrepel', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'photobiology', 'ggplot2', 'photobiologyWavebands', 'ggrepel',
  'lubridate', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'Hmisc', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggcorrplot', 'ggplot2', 'ggrepel', 'ggside', 'ggsignif',
  'paletteer', 'patchwork', 'purrr', 'statsExpressions', 'tidyr'

Packages suggested but not available for checking:
  'afex', 'BayesFactor', 'gapminder', 'lme4', 'metaBMA', 'metaplus',
  'testthat', 'tibble', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom.helpers', 'dplyr', 'forcats', 'ggplot2', 'patchwork', 'purrr',
  'stringr', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'labelled', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'purrr', 'dplyr', 'tidyr', 'forcats'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'patchwork', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'tidycmprsk', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'reshape2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'latex2exp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'gridtext'

Packages suggested but not available for checking:
  'cowplot', 'dplyr', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tidyr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'tibble', 'tidyr', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'tidyr', 'tibble', 'dplyr', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘AICcmodavg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘viridis’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'aplot', 'forcats'

Packages suggested but not available for checking:
  'testthat', 'plotly', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: 'lubridate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'gridtext'

Packages suggested but not available for checking:
  'testthat', 'ggrepel', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pedigreemm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gh', 'lubridate', 'purrr', 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'styler', 'usethis', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'refund', 'testthat', 'ggplot2', 'reshape2', 'dplyr', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Note: skipping ‘ghcm.Rmd’ due to unavailable dependencies:
  'refund', 'ggplot2', 'reshape2', 'dplyr', 'tidyr'
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'testthat', 'cowplot'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ghibli.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ghibli.Rcheck/vign_test/ghibli/vignettes/ghibli_files/figure-html/palettes-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28467 bytes
Input file size = 28581 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 25299
  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 = 25299

Output IDAT size = 25299 bytes (3168 bytes decrease)
Output file size = 25377 bytes (3204 bytes = 11.21% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ghibli.Rcheck/vign_test/ghibli/vignettes/ghibli_files/figure-html/palettes-2.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8461 bytes
Input file size = 8551 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7194
  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 = 7194

Output IDAT size = 7194 bytes (1267 bytes decrease)
Output file size = 7272 bytes (1279 bytes = 14.96% decrease)


Quitting from lines 43-53 [ggplot-marnie] (ghibli.Rmd)
Error: processing vignette 'ghibli.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘ghibli.Rmd’

SUMMARY: processing the following file failed:
  ‘ghibli.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘httr2’

Packages suggested but not available for checking: 'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'purrr', 'dplyr', 'reshape2'

Packages suggested but not available for checking:
  'igraph', 'ggplot2', 'ggraph', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'readr'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'stringr'

Packages suggested but not available for checking: 'rvest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'ggplot2', 'gapminder'
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running examples in ‘gifti-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_binary_datatype
> ### Title: Convert Binary Data Type
> ### Aliases: convert_binary_datatype
> 
> ### ** Examples
> 
> convert_binary_datatype()
$size
[1] 1

$what
integer(0)

> convert_binary_datatype('NIFTI_TYPE_INT32')
$size
[1] 4

$what
integer(0)

> testthat::expect_error(convert_binary_datatype('NIFTI_TYPE_BLAH'))
Error in loadNamespace(x) : there is no package called ‘testthat’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'httr2', 'phytools', 'purrr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', 'patchwork', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gigg.Rd:70-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gigg.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available:
  'dplyr', 'dynutils', 'purrr', 'readr', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'graphicalVAR', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'ggpubr', 'rstatix', 'stringr',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'qgraph', 'MIIVsem', 'imputeTS', 'nloptr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) significantTau.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) significantTau.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DescTools', 'ggplot2'
Running examples in ‘giniVarCI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fcompareCI
> ### Title: Comparisons of variance estimates and confidence intervals for
> ###   the Gini index in finite populations
> ### Aliases: fcompareCI
> 
> ### ** Examples
> 
> # Income and weights (region 'Burgenland') from the 2006 Austrian EU-SILC (Package 'laeken').
> data(eusilc, package="laeken")
> y <- eusilc$eqIncome[eusilc$db040 == "Burgenland"]
> w <- eusilc$rb050[eusilc$db040 == "Burgenland"]
> 
> # Estimation of the Gini index and confidence intervals using different methods.
> fcompareCI(y, w)
Error in loadNamespace(x) : there is no package called ‘ggplot2’
Calls: fcompareCI ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GiniVarInterval.Rmd’ using rmarkdown

Quitting from lines 125-137 [unnamed-chunk-4] (GiniVarInterval.Rmd)
Error: processing vignette 'GiniVarInterval.Rmd' failed with diagnostics:
there is no package called 'DescTools'
--- failed re-building ‘GiniVarInterval.Rmd’

SUMMARY: processing the following file failed:
  ‘GiniVarInterval.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat', 'tibble', 'tidyr'
Running examples in ‘gips-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.gips
> ### Title: Plot optimized matrix or optimization 'gips' object
> ### Aliases: plot.gips
> 
> ### ** Examples
> 
> require("MASS") # for mvrnorm()
Loading required package: MASS
> 
> perm_size <- 6
> mu <- runif(6, -10, 10) # Assume we don't know the mean
> sigma_matrix <- matrix(
+   data = c(
+     1.0, 0.8, 0.6, 0.4, 0.6, 0.8,
+     0.8, 1.0, 0.8, 0.6, 0.4, 0.6,
+     0.6, 0.8, 1.0, 0.8, 0.6, 0.4,
+     0.4, 0.6, 0.8, 1.0, 0.8, 0.6,
+     0.6, 0.4, 0.6, 0.8, 1.0, 0.8,
+     0.8, 0.6, 0.4, 0.6, 0.8, 1.0
+   ),
+   nrow = perm_size, byrow = TRUE
+ ) # sigma_matrix is a matrix invariant under permutation (1,2,3,4,5,6)
> number_of_observations <- 13
> Z <- MASS::mvrnorm(number_of_observations, mu = mu, Sigma = sigma_matrix)
> S <- cov(Z) # Assume we have to estimate the mean
> 
> g <- gips(S, number_of_observations)
> if (require("graphics")) {
+   plot(g, type = "MLE")
+ }
Error in plot(g, type = "MLE") : 
  The packages "dplyr", "tidyr", "tibble", and "ggplot2" are required to
use `plot.gips()` with `type %in% c('heatmap', 'MLE', 'block_heatmap')`;
without those packages, the `stats::heatmap()` will be used
Calls: plot -> plot.gips -> <Anonymous>
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'dplyr', 'eurostat', 'ggplot2', 'httr2', 'testthat'
Running examples in ‘giscoR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gisco_countrycode
> ### Title: Data frame with different country code schemes and world regions
> ### Aliases: gisco_countrycode
> 
> ### ** Examples
> 
> 
> data("gisco_countrycode")
> dplyr::glimpse(gisco_countrycode)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'RecordLinkage', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'igraph', 'purrr', 'reshape2', 'stringr', 'tibble',
  'tidygraph', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘efficiency.Rmd’ using rmarkdown

Quitting from lines 17-137 [setup] (efficiency.Rmd)
Error: processing vignette 'efficiency.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘efficiency.Rmd’

--- re-building ‘plain_text.Rmd’ using rmarkdown
--- finished re-building ‘plain_text.Rmd’

--- re-building ‘split_by.Rmd’ using rmarkdown

Quitting from lines 17-141 [setup] (split_by.Rmd)
Error: processing vignette 'split_by.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘split_by.Rmd’

--- re-building ‘version_control.Rmd’ using rmarkdown
--- finished re-building ‘version_control.Rmd’

--- re-building ‘workflow.Rmd’ using rmarkdown
--- finished re-building ‘workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘efficiency.Rmd’ ‘split_by.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'mockery', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘helper-survey.Rmd’ using rmarkdown
--- finished re-building ‘helper-survey.Rmd’

--- re-building ‘package.Rmd’ using rmarkdown

Quitting from lines 113-124 [unnamed-chunk-2] (package.Rmd)
Error: processing vignette 'package.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building ‘package.Rmd’

SUMMARY: processing the following file failed:
  ‘package.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'purrr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'stringr', 'mockery'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'shinyFiles', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'mockery'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'gh'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'targets', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) gjamCensorY.Rd:27: Lost braces; missing escapes or markup?
    27 |   \item{\code{y}}{n by S matrix updated with censored {values} substituted for
       |                                                       ^
checkRd: (-1) gjamFillMissingTimes.Rd:32: Lost braces
    32 | Missing times in the data occur where there are gaps in \code{timeCol} column of \code{xdata} and the initial time \code{0} for each sequence.  New versions of the data have \code{NA} (\code{xdata}) or prior values with appropriate weight (\code{ydata}).  Missing times are filled in \code{xdata, ydata, edata}, including a time \code{0} which serves as a prior mean for \code{ydata} for time code{1}.  The group and time indices in columns \code{groupCol} and \code{timeCol} of \code{xdata} reference the time for a given time series.  Missing values in the columns \code{groupVars} of \code{xdata} are filled automatically filled in.  This assumes that values for these variables are fixed for the group.  If \code{FILLMEANS}, the missing  values in \code{ydata} are filled with means for the group and given a low weight specified in \code{missingEffort}.
       |                                                                                                                                                                                                                                                                                                                                                                                                              ^
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'Ecdat', 'lubridate', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) GeneralisedLambdaDistribution.Rd:60: Lost braces; missing escapes or markup?
    60 |   \code{gpd} uses GPD parameterisation, see {van Staden and Loots (2009)}
       |                                             ^
checkRd: (-1) gld.lmoments.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.lmoments.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.lmoments.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.lmoments.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.moments.Rd:14: Lost braces
    14 |   {\eqn{\lambda_1}{lambda 1} location parameter}
       |   ^
checkRd: (-1) gld.moments.Rd:15: Lost braces
    15 |   {\eqn{\lambda_2}{lambda 2} - scale parameter}
       |   ^
checkRd: (-1) gld.moments.Rd:16: Lost braces
    16 |   {\eqn{\lambda_3}{lambda 3} - first shape parameter}
       |   ^
checkRd: (-1) gld.moments.Rd:17: Lost braces
    17 |   {\eqn{\lambda_4}{lambda 4} - second shape parameter}
       |   ^
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘optimx’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NEWS.Rd:16: Lost braces; missing escapes or markup?
    16 |         \item Now \code{AICc == Inf} when {n <= p + 1}.
       |                                           ^
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'lme4', 'lmerTest'
checkRd: (-1) summarylr.Rd:34: Lost braces
    34 | \item{method}{NULL or character vector of length 0, 1 or 2; may be code{"LRT"} or \code{"Rao"} or \code{c("LRT", "Rao")} to compute specified P-values.
       |                                                                        ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'pkgdown', 'effects', 'DHARMa'
Packages required but not available:
  'cowplot', 'ggforce', 'ggplot2', 'glmmTMB', 'lme4'

Packages suggested but not available for checking:
  'cosinor', 'DHARMa', 'dplyr', 'ftExtra', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘mlmRev’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'broom.mixed', 'dplyr', 'forcats', 'ggplot2', 'loo',
  'reshape2', 'rstan', 'tibble'

Packages suggested but not available for checking:
  'bayesplot', 'testthat', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Packages required but not available:
  'lme4', 'ggplot2', 'reshape2', 'rstan', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmmrBase’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'ggplot2', 'ggpubr', 'glmmTMB', 'lme4', 'lmerTest', 'plotly',
  'qvalue'

Packages suggested but not available for checking: 'kableExtra', 'DESeq2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'mlmRev', 'reshape2', 'car', 'DHARMa',
  'effects', 'dotwhisker', 'broom', 'broom.mixed', 'huxtable', 'blme',
  'purrr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Coxnet.Rmd’ using rmarkdown
--- finished re-building ‘Coxnet.Rmd’

--- re-building ‘glmnet.Rmd’ using rmarkdown
--- finished re-building ‘glmnet.Rmd’

--- re-building ‘glmnetFamily.Rmd’ using rmarkdown

Quitting from lines 96-106 [unnamed-chunk-5] (glmnetFamily.Rmd)
Error: processing vignette 'glmnetFamily.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building ‘glmnetFamily.Rmd’

--- re-building ‘relax.Rmd’ using rmarkdown
--- finished re-building ‘relax.Rmd’

SUMMARY: processing the following file failed:
  ‘glmnetFamily.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'smoof', 'mlrMBO', 'randomForestSRC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv(R_TESTS="")  # needed for cluster creation to work
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'effects', 'AER', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'logisticPCA', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘glmpca.Rmd’ using knitr

Quitting from lines 13-15 [unnamed-chunk-1] (glmpca.Rmd)
Error: processing vignette 'glmpca.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘glmpca.Rmd’

SUMMARY: processing the following file failed:
  ‘glmpca.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'AER', 'mlogit', 'dfidx', 'lme4'

Packages suggested but not available for checking: 'ggplot2', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                            ^
checkRd: (-1) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                                                ^
checkRd: (-1) galapagos.Rd:4: Lost braces
     4 | \title{{Gal\'{a}pagos} Island species data}
       |              ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                      ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |    ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |          ^
checkRd: (-1) galapagos.Rd:44: Lost braces
    44 |   Species number and endemism: The {Gal\'{a}pagos} Archipelago revisited.
       |                                          ^
Packages required but not available: 'stringr', 'dplyr', 'ggplot2', 'cplm'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'caret'

Packages suggested but not available for checking: 'FactoMineR', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:14: Lost braces
    14 |   \item{object}{A fitted model object, of class \code{glm}, \code{lm} or code{glm.nb}}
       |                                                                              ^
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-methods.Rd:14: Lost braces
    14 | code{glmulti} finds what are the \code{n} best models (the confidence set of models) among all possible models (the candidate set, as specified by the user).
       |     ^
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘AER’
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'dbplyr', 'dplyr', 'forcats', 'forecast', 'ggplot2', 'gtrendsR',
  'lubridate', 'purrr', 'RSQLite', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'genlasso', 'fda', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fxregime’
Unavailable namespace imported from by a ':::' call: ‘fxregime’
  See the note in ?`:::` about the use of this operator.
Packages required but not available: 'kableExtra', 'rvest'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr', 'purrr'

Packages suggested but not available for checking: 'testthat', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'readxl', 'tibble', 'tidyr', 'tmap'

Packages suggested but not available for checking: 'mapedit', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getRiiGLPK.Rd:35: Lost braces; missing escapes or markup?
    35 |   Returns the current scale factor $r_{ii}$ for row \code{i} of the specified
       |                                       ^
checkRd: (-1) getSjjGLPK.Rd:35: Lost braces; missing escapes or markup?
    35 |   Returns the current scale factor $s_{jj}$ for column \code{j} of the
       |                                       ^
checkRd: (-1) setRiiGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $r_{ii}$.
       |                     ^
checkRd: (-1) setSjjGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $s_{jj}$.
       |                     ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mvSLOUCH’
Running examples in ‘GLSME-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GLSME-package
> ### Title: Generalized Least Squares with Measurement Error
> ### Aliases: GLSME-package
> ### Keywords: generalized least squares regression measurement error
> 
> ### ** Examples
> 
> n<-3 ## number of species
> apetree<-ape::rtree(n)
> ### Define Brownian motion parameters to be able to simulate data under the Brownian motion model.
> BMparameters<-list(vX0=matrix(0,nrow=2,ncol=1),Sxx=rbind(c(1,0),c(0.2,1)))
> ### Now simulate the data and remove the values corresponding to the internal nodes.
> xydata<-mvSLOUCH::simulBMProcPhylTree(apetree,X0=BMparameters$vX0,Sigma=BMparameters$Sxx)
Error in loadNamespace(x) : there is no package called ‘mvSLOUCH’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'rvest', 'stringr', 'testthat'
Running examples in ‘gluedown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: md_paragraph
> ### Title: Markdown paragraphs breaks
> ### Aliases: md_paragraph
> 
> ### ** Examples
> 
> md_paragraph(stringr::sentences[1:3])
Error in loadNamespace(x) : there is no package called ‘stringr’
Calls: md_paragraph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘github-spec.Rmd’ using rmarkdown

Quitting from lines 21-24 [setup] (github-spec.Rmd)
Error: processing vignette 'github-spec.Rmd' failed with diagnostics:
there is no package called 'stringr'
--- failed re-building ‘github-spec.Rmd’

--- re-building ‘literal-programming.Rmd’ using rmarkdown

Quitting from lines 20-24 [libraries] (literal-programming.Rmd)
Error: processing vignette 'literal-programming.Rmd' failed with diagnostics:
there is no package called 'stringr'
--- failed re-building ‘literal-programming.Rmd’

SUMMARY: processing the following files failed:
  ‘github-spec.Rmd’ ‘literal-programming.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'RSQLite', 'testthat', 'vctrs', 'waldo'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘engines.Rmd’ using rmarkdown

Quitting from lines 55-58 [unnamed-chunk-4] (engines.Rmd)
Error: processing vignette 'engines.Rmd' failed with diagnostics:
error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'RSQLite'
--- failed re-building ‘engines.Rmd’

--- re-building ‘transformers.Rmd’ using rmarkdown
hello!
Loading required package: emo
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'emo'
--- finished re-building ‘transformers.Rmd’

SUMMARY: processing the following file failed:
  ‘engines.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rematch2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Hmisc', 'testthat'
checkRd: (-1) rtheta.Rd:50-76: Lost braces in \itemize; meant \describe ?
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Note: skipping ‘GMCM-JStatSoft.Rnw’ due to unavailable dependencies:
  'Hmisc'
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'gsDesign', 'gt', 'kableExtra', 'testthat', 'tibble'

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.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DescTools', 'readxl'
checkRd: (-1) Maf.data.frame.Rd:65: Lost braces
    65 | the lag distance to take. \%For other options see code{getEmpVariogramSlice}.}
       |                                                       ^
checkRd: (-1) NGSAustralia.Rd:114: Lost braces; missing escapes or markup?
   114 | \item{MRB}{obtained from simplifying the major crustal boundaries of {Korsch2015a, Korsch2015b}}
       |                                                                      ^
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmlTable', 'Hmisc', 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'SeqVarTools', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘car’
checkRd: (-1) ATEgel.Rd:24: Lost braces
    24 | \item{g}{A formula as \code{y~z}, where code{y} is the response and
       |                                             ^
Note: skipping ‘gmm_with_R.rnw’ due to unavailable dependencies: 'car'
Package required but not available: ‘mlogit’

Packages suggested but not available for checking: 'AER', 'car', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Packages required but not available:
  'ggrepel', 'ggplot2', 'tidyselect', 'tidyr', 'tibble', 'purrr',
  'dplyr'

Packages suggested but not available for checking:
  'roxygen2', 'ggsci', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'mvp'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magick', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking: 'qgraph', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GFDmcv', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘wv’

Package suggested but not available for checking: ‘simts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggforce', 'ggplot2', 'ggpubr', 'igraph', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GNE.ceq.Rd:50: Lost braces
    50 | (KKT) system denoted by \eqn{H(z)=0}, for \eqn{z \in \Omega} where eqn{z} is formed by the players strategy 
       |                                                                       ^
checkRd: (-1) GNE.nseq.Rd:76: Lost braces
    76 | (KKT) system denoted by \eqn{\Phi(z)=0}{Phi(z)=0}, where eqn{z} is formed by the players strategy 
       |                                                             ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'vcdExtra'
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'keras', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'devtools'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tibble', 'tidyselect', 'tidyr', 'readxl', 'vctrs',
  'ggplot2', 'treemap', 'igraph', 'ggraph'

Packages suggested but not available for checking:
  'AnnotationDbi', 'GO.db', 'org.Hs.eg.db', 'fgsea', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggrepel', 'igraph', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'vegdata', 'BiodiversityR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rrpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'epiR', 'stringr'

Packages suggested but not available for checking:
  'dfidx', 'mlogit', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'yarrr', 'progress'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘fda.usc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'pixiedust', 'igraph', 'ggraph', 'migraph',
  'manynet', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'dockerfiler', 'pkgdown', 'purrr', 'roxygen2', 'stringr',
  'testthat', 'attachment', 'usethis'
checkRd: (-1) create_golem.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
checkRd: (-1) fill_desc.Rd:42: Lost braces; missing escapes or markup?
    42 | The {desc} object, invisibly.
       |     ^
checkRd: (-1) get_sysreqs.Rd:23: Lost braces; missing escapes or markup?
    23 | {dockerfiler}.
       | ^
checkRd: (-1) golem_opts.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{config_file}{path to the {golem} config file}
       |                                ^
checkRd: (-1) install_dev_deps.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {golem} dev dependencies}
       |                ^
checkRd: (-1) project_hook.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{package_name}{Package name to use. By default, {golem} uses
       |                                                      ^
Running ‘manualtests.R’ [0s/1s]
  Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘a_start.Rmd’ using rmarkdown

Quitting from lines 67-70 [unnamed-chunk-5] (a_start.Rmd)
Error: processing vignette 'a_start.Rmd' failed with diagnostics:
The package "usethis" (>= 1.6.0) is required to check the package name.
--- failed re-building ‘a_start.Rmd’

--- re-building ‘b_dev.Rmd’ using rmarkdown
--- finished re-building ‘b_dev.Rmd’

--- re-building ‘c_deploy.Rmd’ using rmarkdown
--- finished re-building ‘c_deploy.Rmd’

--- re-building ‘d_js.Rmd’ using rmarkdown
--- finished re-building ‘d_js.Rmd’

--- re-building ‘e_config.Rmd’ using rmarkdown

Quitting from lines 11-25 [unnamed-chunk-1] (e_config.Rmd)
Error: processing vignette 'e_config.Rmd' failed with diagnostics:
The package "usethis" (>= 1.6.0) is required to check the package name.
--- failed re-building ‘e_config.Rmd’

--- re-building ‘f_extending_golem.Rmd’ using rmarkdown
--- finished re-building ‘f_extending_golem.Rmd’

--- re-building ‘z_golem_cheatsheet.Rmd’ using rmarkdown
--- finished re-building ‘z_golem_cheatsheet.Rmd’

SUMMARY: processing the following files failed:
  ‘a_start.Rmd’ ‘e_config.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'broom', 'cowplot', 'dplyr', 'flexsurv', 'ggplot2', 'ggsci',
  'modelr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'socviz', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'imager', 'concaveman'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'car'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GoodmanKruskal.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GoodmanKruskal.Rcheck/vign_test/GoodmanKruskal/vignettes/GoodmanKruskal_files/figure-html/unnamed-chunk-4-1.png
720x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 84173 bytes
Input file size = 84371 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 70276
  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 = 70276

Output IDAT size = 70276 bytes (13897 bytes decrease)
Output file size = 70354 bytes (14017 bytes = 16.61% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GoodmanKruskal.Rcheck/vign_test/GoodmanKruskal/vignettes/GoodmanKruskal_files/figure-html/unnamed-chunk-5-1.png
720x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 94367 bytes
Input file size = 94577 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 77902
  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 = 77902

Output IDAT size = 77902 bytes (16465 bytes decrease)
Output file size = 77980 bytes (16597 bytes = 17.55% decrease)


Quitting from lines 148-151 (GoodmanKruskal.Rmd)
Error: processing vignette 'GoodmanKruskal.Rmd' failed with diagnostics:
object 'Greene' not found
--- failed re-building ‘GoodmanKruskal.Rmd’

SUMMARY: processing the following file failed:
  ‘GoodmanKruskal.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown

Quitting from lines 51-64 [unnamed-chunk-5] (basics.Rmd)
Error: processing vignette 'basics.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘basics.Rmd’

SUMMARY: processing the following file failed:
  ‘basics.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'purrr', 'tibble', 'tidyr', 'usethis'

Packages suggested but not available for checking:
  'bigQueryR', 'ganalytics', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'googleAnalyticsR', 'roxygen2', 'testthat', 'usethis'
Package required but not available: ‘usethis’

Packages suggested but not available for checking: 'targets', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'readr', 'testthat', 'usethis'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking: 'testthat', 'mockery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'pillar', 'purrr', 'tibble', 'vctrs'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pkgdown', 'testthat'
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rvest’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'purrr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'rvest', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'readr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘readxl’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cellranger', 'googledrive', 'purrr', 'rematch2', 'tibble', 'vctrs'

Packages suggested but not available for checking: 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'ColorNameR', 'schemr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) google_find_place.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_find_place.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_find_place.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) google_map.Rd:54: Lost braces; missing escapes or markup?
    54 | of `{sf}` objects).}
       |     ^
Running ‘manual_tests.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'ggdendro'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BradleyTerry2', 'DescTools', 'ggplot2', 'ggparty', 'ggrepel',
  'PlackettLuce', 'tidyr', 'patchwork'

Package suggested but not available for checking: ‘climatrends’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'httr2', 'janitor', 'lubridate', 'stringr', 'tidyr'

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: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'GO.db', 'ggraph', 'igraph', 'network', 'dplyr', 'biomaRt',
  'annotate', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gms’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tidyr', 'purrr', 'tibble', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'cowplot'

Package suggested but not available for checking: ‘testthat’

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: 'fda', 'fda.usc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) solve_game.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) solve_game.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following HTML validation problems:
exponential_anisotropic3D_alt.html:70:1 (exponential_anisotropic3D_alt.Rd:34): Warning: trimming empty <h3>
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'RSQLite', 'dplyr', 'dbplyr'
Running examples in ‘gpkg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gpkg_table_pragma
> ### Title: Lazy Access to Tables by Name
> ### Aliases: gpkg_table_pragma gpkg_table_pragma.character
> ###   gpkg_table_pragma.SQLiteConnection gpkg_table_pragma.geopackage
> ###   gpkg_table gpkg_table.default gpkg_collect gpkg_tbl gpkg_rast
> ###   gpkg_vect
> 
> ### ** Examples
> 
> ## Don't show: 
> if (!inherits(try(requireNamespace("RSQLite", quietly = TRUE)), 'try-error') &&!inherits(try(requireNamespace("dbplyr", quietly = TRUE)), 'try-error') && !inherits(try(requireNamespace("terra", quietly = TRUE)), 'try-error')) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
> ## End(Don't show)
> 
> tf <- tempfile(fileext = ".gpkg")
> 
> r <- terra::rast(system.file("extdata", "dem.tif", package = "gpkg"))
> 
> gpkg_write(r,
+            destfile = tf,
+            RASTER_TABLE = "DEM1",
+            FIELD_NAME = "Elevation")
> 
> gpkg_write(r,
+            destfile = tf,
+            append = TRUE,
+            RASTER_TABLE = "DEM2",
+            FIELD_NAME = "Elevation")
> 
> g <- geopackage(tf)
Error: package `RSQLite` is required to get the `gpkg_contents` table
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
gpkg_bbox 6.078  0.043   7.398
Running ‘tinytest.R’ [1s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("gpkg")
  + }
  
  test_gpkg.R...................    0 tests    Error in eval(expr, envir = e) : 
    requireNamespace("RSQLite", quietly = TRUE) is not TRUE
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> stopifnot
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown

Quitting from lines 35-61 [unnamed-chunk-2] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
package `RSQLite` is required to set `data_null`
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown

Quitting from lines 35-38 [unnamed-chunk-2] (quickstart.Rmd)
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:21: Lost braces
    21 |     in code{data} not in this list will be ignored. Use \code{NA} to
       |            ^
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) Auxil.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Auxil.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Fit.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Predict.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'plotly', 'tidyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'nbpMatching'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet.extras', 'purrr', 'suncalc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cmdstanr’
Packages required but not available:
  'httr2', 'purrr', 'rvest', 'shiny.i18n', 'SSEparser', 'stringr'

Packages suggested but not available for checking: 'shinytest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'httr2', 'tidyr'

Packages suggested but not available for checking: 'httptest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tensorflow’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'rvest', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pryr’

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggthemes', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) grade-package.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:58-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:79-81: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'car', 'Hmisc', 'lme4', 'lmerTest', 'patchwork', 'purrr',
  'tidyr'

Packages suggested but not available for checking:
  'dplyr', 'pbkrtest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lime’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRbase', 'igraph', 'broom'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'igraph'

Packages suggested but not available for checking:
  'cowplot', 'ggthemes', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'patchwork', 'reshape2', 'cowplot'

Packages suggested but not available for checking:
  'Seurat', 'ggrepel', 'DESeq2', 'clusterProfiler', 'biomaRt',
  'msigdbr', 'fgsea', 'monocle', 'ggrastr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Granger.inference.difference.Rd:65: Lost braces; missing escapes or markup?
    65 |         least one root larger than one) on bootstrapped \verb{x} and {y}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:68: Lost braces; missing escapes or markup?
    68 |         least one root larger than one) on bootstrapped \verb{x} and {z}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:71: Lost braces; missing escapes or markup?
    71 |         least one root larger than one) on bootstrapped \verb{x}, \verb{y} and {z}.
       |                                                                                ^
Packages required but not available: 'dplyr', 'ggplot2', 'tibble', 'tidyr'

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:
  'tibble', 'vctrs', 'dplyr', 'tidyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'kableExtra', 'summarytools', 'dplyr', 'ggpubr', 'Hmisc', 'ggplot2',
  'reshape2', 'desplot', 'PairedData'

Packages suggested but not available for checking: 'shinytest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'adegenet', 'ggplot2', 'stringr', 'igraph', 'tidyr', 'hierfstat',
  'gdistance', 'ecodist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sparklyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'edmcr'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'dplyr', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'testthat', 'ggraph', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Packages required but not available:
  'ggplot2', 'ggrepel', 'reshape2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'devtools', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'igraph', 'purrr', 'tidyr'

Packages suggested but not available for checking: 'rtweet', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'vctrs', 'testthat'
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘grates.Rmd’ using knitr

Quitting from lines 113-133 [unnamed-chunk-3] (grates.Rmd)
Error: processing vignette 'grates.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘grates.Rmd’

SUMMARY: processing the following file failed:
  ‘grates.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'tibble', 'dplyr', 'tidyr', 'patchwork', 'vctrs', 'purrr',
  'stringr', 'tidyselect', 'pillar', 'ggokabeito'

Packages suggested but not available for checking:
  'gamm4', 'lme4', 'testthat', 'vdiffr', 'forcats', 'GJRM', 'readr',
  'glmmTMB', 'ggdist', 'distributional'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘graticule.Rmd’ using rmarkdown
** Processing: README-unnamed-chunk-3-1.png
864x864 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 117470 bytes
Input file size = 117716 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 97138
  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 = 97138

Output IDAT size = 97138 bytes (20332 bytes decrease)
Output file size = 97216 bytes (20500 bytes = 17.41% decrease)

** Processing: README-unnamed-chunk-4-1.png
864x864 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 172491 bytes
Input file size = 172821 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 140431
  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 = 140431

Output IDAT size = 140431 bytes (32060 bytes decrease)
Output file size = 140509 bytes (32312 bytes = 18.70% decrease)


Quitting from lines 156-157 [unnamed-chunk-5] (graticule.Rmd)
Error: processing vignette 'graticule.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘graticule.Rmd’

SUMMARY: processing the following file failed:
  ‘graticule.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'feasts', 'forecast', 'purrr', 'tibble', 'tsfeatures',
  'tsibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'distributional', 'fable', 'fabletools'
Package required but not available: ‘forecast’

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRain', 'gRbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'dplyr', 'tsibble', 'tibble', 'tidyr', 'ggplot2',
  'stringr', 'lvplot', 'ggridges'

Packages suggested but not available for checking:
  'tsibbledata', 'purrr', 'testthat', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr', 'purrr'

Packages suggested but not available for checking: 'testthat', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo_vignette.Rmd’ using rmarkdown

Quitting from lines 210-234 [plot.section067] (demo_vignette.Rmd)
Error: processing vignette 'demo_vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘demo_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘demo_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRbase', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'furrr', 'ggplot2', 'patchwork'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'igraph', 'tidygraph', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MinimiseEPL.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MinimiseEPL.Rd:20: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'nbpMatching', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'swirlify', 'swirl', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'ggplot2', 'plotly', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'ggplot2', 'dplyr', 'tmap', 'tidyselect', 'networkD3'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Gmisc', 'broom', 'Epi', 'dplyr', 'htmlTable', 'Hmisc', 'purrr',
  'rms', 'stringr', 'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) covFun.Rd:89-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:91-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:93-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:96-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:98-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:100-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:116-117: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'rms', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'greta', 'tensorflow'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'greta', 'tensorflow'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'progress', 'tensorflow'

Packages suggested but not available for checking:
  'bayesplot', 'DiagrammeR', 'ggplot2', 'mockery', 'testthat',
  'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

Packages suggested but not available for checking: 'smooth', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'plotly', 'ggplot2', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DiagrammeR', 'rdd', 'testthat'
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Packages suggested but not available for checking:
  'ggplot2', 'egg', 'testthat'
Package suggested but not available for checking: ‘magick’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'ggplot2', 'magick', 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shinytest2’
Running ‘testthat.R’ [0s/0s]
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
checkRd: (-1) NEWS.Rd:669: Lost braces; missing escapes or markup?
   669 |     parameters are rounded so they belong to one of {0, 0.5, 1}. (Simon)
       |                                                     ^
checkRd: (-1) gradients.Rd:96-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:100-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:104-107: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘stringr’

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRbase', 'doBy', 'igraph', 'gRain'

Package suggested but not available for checking: ‘testthat’

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: ‘usethis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'dplyr', 'tidyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'rearrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'ggplot2', 'lmerTest', 'testthat', 'xpectr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qvalue’

Package suggested but not available for checking: ‘snplist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clusterProfiler', 'dplyr', 'org.Mm.eg.db', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'stringr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'vctrs', 'pillar', 'purrr', 'tidyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘GroupSeq.Rmd’ using rmarkdown

Quitting from lines 17-39 [knitr-setup] (GroupSeq.Rmd)
Error: processing vignette 'GroupSeq.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘GroupSeq.Rmd’

--- re-building ‘task-1-compute-bounds-H0.Rmd’ using rmarkdown
--- finished re-building ‘task-1-compute-bounds-H0.Rmd’

--- re-building ‘task-2-compute-drift.Rmd’ using rmarkdown
--- finished re-building ‘task-2-compute-drift.Rmd’

--- re-building ‘task-3-compute-bounds-H1.Rmd’ using rmarkdown
--- finished re-building ‘task-3-compute-bounds-H1.Rmd’

--- re-building ‘task-4-compute-CI.Rmd’ using rmarkdown
--- finished re-building ‘task-4-compute-CI.Rmd’

--- re-building ‘understanding-gs-designs.Rmd’ using rmarkdown

Quitting from lines 18-41 [knitr-setup] (understanding-gs-designs.Rmd)
Error: processing vignette 'understanding-gs-designs.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘understanding-gs-designs.Rmd’

SUMMARY: processing the following files failed:
  ‘GroupSeq.Rmd’ ‘understanding-gs-designs.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'patchwork', 'testthat'
Running examples in ‘growR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_lines
> ### Title: Add data to a ggplot
> ### Aliases: add_lines
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tidyr', 'dplyr', 'labelled'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ##
  > ##  Unit testing file
  > ##
  > ##  Created by Daniel Rodríguez Pérez on 7/12/2014.
  > ##
  > ##  Copyright (c) 2014 Daniel Rodríguez Pérez.
  > ##
  > ##  This program is free software: you can redistribute it and/or modify
  > ##  it under the terms of the GNU General Public License as published by
  > ##  the Free Software Foundation, either version 3 of the License, or
  > ##  (at your option) any later version.
  > ##
  > ##  This program is distributed in the hope that it will be useful,
  > ##  but WITHOUT ANY WARRANTY; without even the implied warranty of
  > ##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > ##  GNU General Public License for more details.
  > ##
  > ##  You should have received a copy of the GNU General Public License
  > ##  along with this program.  If not, see <http://www.gnu.org/licenses/>
  > ## 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dae', 'GGally', 'ggplot2', 'Hmisc', 'JOPS', 'readxl'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'ggplot2'
checkRd: (-1) predict.Rd:30: Lost braces
    30 | resp. code{'exponential'} or \code{'no_lag'} for \code{fit_easylinear}.}
       |           ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DiagrammeR', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Birthwt.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Birthwt.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Lung.Rd:36-38: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'SLOPE'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
checkRd: (-1) matches.Rd:33: Lost braces; missing escapes or markup?
    33 | be set to an index value of \code{length+1}.  If {indexes=FALSE}, they will
       |                                                  ^
Packages required but not available:
  'ggplot2', 'dplyr', 'readr', 'tidyr', 'stringr', 'purrr', 'gt'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GRS.Powerfunc.Rd:22: Lost braces
    22 | {Power: }{Matrix of power values plotted}
       |          ^
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
checkRd: (-1) qdb.p.correct.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{refpts}{a numeric vector used as a reference point to determine the correct side of the \code{qdb} for classifying \code{x}. The \code{length(refpts)} should be equal to {ncol(x)}. Default to \code{colMeans(x)}. }
       |                                                                                                                                                                                 ^
Packages required but not available:
  'dplyr', 'tidyr', 'lubridate', 'stringr', 'ggplot2'

Packages suggested but not available for checking:
  'ggridges', 'ggHoriPlot', 'ggthemes', 'kableExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gsDesign', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'igraph', 'missSBM', 'testthat'
checkRd: (-1) crossval.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crossval.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gsbm_mcgd_parallel.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
Error(s) in re-building vignettes:
  ...
--- re-building ‘PrimarySchool.Rmd’ using rmarkdown

Quitting from lines 21-33 [load data] (PrimarySchool.Rmd)
Error: processing vignette 'PrimarySchool.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘PrimarySchool.Rmd’

--- re-building ‘blogosphere.Rmd’ using rmarkdown

Quitting from lines 22-32 [load data] (blogosphere.Rmd)
Error: processing vignette 'blogosphere.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘blogosphere.Rmd’

--- re-building ‘les_miserables.Rmd’ using rmarkdown

Quitting from lines 18-22 [setup] (les_miserables.Rmd)
Error: processing vignette 'les_miserables.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘les_miserables.Rmd’

SUMMARY: processing the following files failed:
  ‘PrimarySchool.Rmd’ ‘blogosphere.Rmd’ ‘les_miserables.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'stringr', 'progress', 'fastDummies', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'gsDesign'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_gscounts.Rmd’ using rmarkdown

Quitting from lines 261-285 [info-monitoring] (Introduction_gscounts.Rmd)
Error: processing vignette 'Introduction_gscounts.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Introduction_gscounts.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_gscounts.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'readr', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'cowplot', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘msigdbr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'gsDesign', 'gt', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'gt', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'aplot', 'DOSE', 'dplyr', 'ggplot2', 'ggpp', 'ggrepel', 'ggsci',
  'purrr', 'reshape2', 'stringr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cellWise', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking: 'testthat', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'imager'
checkRd: (-1) besselap.Rd:58: Lost braces
    58 | Thomas Sailer, email{t.sailer@alumni.ethz.ch}.\cr Conversion to R by
       |                     ^
checkRd: (-1) diric.Rd:25: Lost braces; missing escapes or markup?
    25 | evaluated at the elements of the input array {x}.
       |                                              ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘ggplot2’
checkRd: (-1) lisiecki2005.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:29: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 64-75 [unnamed-chunk-6] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- 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: ‘testthat’
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat', 'tidyr', 'roxyglobals'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'FactoMineR', 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'patchwork', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) jura.Rd:29: Lost braces; missing escapes or markup?
    29 |         \item{Cd}{ mg cadmium kg^{-1} topsoil }
       |                                  ^
checkRd: (-1) jura.Rd:30: Lost braces; missing escapes or markup?
    30 |         \item{Co}{ mg cobalt kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:31: Lost braces; missing escapes or markup?
    31 |         \item{Cr}{ mg chromium kg^{-1} topsoil }
       |                                   ^
checkRd: (-1) jura.Rd:32: Lost braces; missing escapes or markup?
    32 |         \item{Cu}{ mg copper kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{Ni}{ mg nickel kg^{-1} topsoil }
       |                                 ^
checkRd: (-1) jura.Rd:34: Lost braces; missing escapes or markup?
    34 |         \item{Pb}{ mg lead kg^{-1} topsoil }
       |                               ^
checkRd: (-1) jura.Rd:35: Lost braces; missing escapes or markup?
    35 |         \item{Zn}{ mg zinc kg^{-1} topsoil }
       |                               ^
checkRd: (-1) variogramST.Rd:49: Lost braces; missing escapes or markup?
    49 |   time lag $t$, the pseudo cross variogram $(Z_i(s)-Z_{i+t}(s+h))^2$ is averaged over all time 
       |                                                       ^
checkRd: (-1) variogramST.Rd:50: Lost braces; missing escapes or markup?
    50 |   lagged observation sets $Z_i$ and $Z_{i+t}$ available (weighted by the number of pairs involved).
       |                                        ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'profvis', 'testthat'
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) artset1987.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gte.Rd:98: Lost braces; missing escapes or markup?
    98 | \code{left} and {right} for illustrative purpose), one would need a third variable (\code{status}) taking the value 0 
       |                 ^
Packages required but not available: 'gt', 'dplyr', 'ggplot2', 'paletteer'

Packages suggested but not available for checking:
  'hms', 'rvest', 'stringr', 'testthat', 'tibble', 'tidyr',
  'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dlookr', 'dplyr', 'igraph', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'furrr', 'gtfs2gps'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘furrr’

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dodgr', 'dplyr', 'ggplot2', 'hms', 'lubridate', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library (testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gtfsrouter.Rmd’ using rmarkdown
--- finished re-building ‘gtfsrouter.Rmd’

--- re-building ‘transfers.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gtfsrouter.Rcheck/vign_test/gtfsrouter/vignettes/transfers_files/figure-html/d_limit1-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44614 bytes
Input file size = 44752 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 35451
  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 = 35451

Output IDAT size = 35451 bytes (9163 bytes decrease)
Output file size = 35529 bytes (9223 bytes = 20.61% decrease)


Quitting from lines 444-487 [travel_times_d_limit-fn] (transfers.Rmd)
Error: processing vignette 'transfers.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘transfers.Rmd’

--- re-building ‘traveltimes.Rmd’ using rmarkdown

Quitting from lines 100-102 [maxtt] (traveltimes.Rmd)
Error: processing vignette 'traveltimes.Rmd' failed with diagnostics:
there is no package called 'hms'
--- failed re-building ‘traveltimes.Rmd’

SUMMARY: processing the following files failed:
  ‘transfers.Rmd’ ‘traveltimes.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'ggplot2', 'testthat'
File ‘gtfstools/libs/gtfstools.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

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: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'SGP', 'taxize'
Package required but not available: ‘gt’

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rvest’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'ggplot2', 'lubridate', 'magick', 'paletteer', 'rvest', 'testthat',
  'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom.helpers', 'dplyr', 'forcats', 'gtsummary', 'purrr', 'stringr',
  'tibble', 'tidyr'

Packages suggested but not available for checking: 'gt', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'broom.helpers', 'dplyr', 'forcats', 'gt', 'purrr',
  'stringr', 'tibble', 'tidyr', 'vctrs'

Packages suggested but not available for checking:
  'broom.mixed', 'car', 'geepack', 'ggstats', 'Hmisc', 'huxtable',
  'kableExtra', 'lme4', 'mice', 'parsnip', 'testthat', 'tidycmprsk',
  'workflows'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tibble'
Error in get(f, envir = code_env) : 
  cannot return a promise (PROMSXP) object
Calls: <Anonymous> -> Filter -> unlist -> lapply -> FUN -> get
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'lubridate', 'ggplot2', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'posterior'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'adespatial', 'car', 'effects', 'ggplot2', 'ggpcp', 'ggrepel',
  'heplots', 'patchwork', 'candisc', 'dplyr', 'tidyr'
Running examples in ‘Guerry-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Guerry
> ### Title: Data from A.-M. Guerry, "Essay on the Moral Statistics of
> ###   France"
> ### Aliases: Guerry
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Angeville 5.722  0.099   9.385
Error(s) in re-building vignettes:
  ...
--- re-building ‘MultiSpat.Rmd’ using rmarkdown

Quitting from lines 41-47 [unnamed-chunk-1] (MultiSpat.Rmd)
Error: processing vignette 'MultiSpat.Rmd' failed with diagnostics:
there is no package called 'adespatial'
--- failed re-building ‘MultiSpat.Rmd’

--- re-building ‘guerry-multivariate.Rmd’ using rmarkdown

Quitting from lines 52-63 [load] (guerry-multivariate.Rmd)
Error: processing vignette 'guerry-multivariate.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building ‘guerry-multivariate.Rmd’

SUMMARY: processing the following files failed:
  ‘MultiSpat.Rmd’ ‘guerry-multivariate.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'network', 'GGally'

Package suggested but not available for checking: ‘sna’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) PLSSVD.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
checkRd: (-1) guidedPLS.Rd:33: Lost braces; missing escapes or markup?
    33 | The number of low-dimension (k < {N, M, L, O}, Default: .minDim(X1, X2, Y1, Y2))
       |                                  ^
checkRd: (-1) sPLSDA.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'readr', 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘RRprof.out’
checkRd: (-1) gumbel.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gumbel.Rd:75: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'stringr', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel'

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'tibble', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'purrr', 'readr', 'stringr'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tidyr', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'drc', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lubridate', 'tsDyn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'eda4treeR', 'lme4'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) esSim.Rd:81: Lost braces; missing escapes or markup?
    81 | \eqn{83} SNPs are in cluster {-}, \eqn{714} SNPs are in cluster \eqn{0},
       |                              ^
checkRd: (-1) esSimDiffPriors.Rd:91: Lost braces; missing escapes or markup?
    91 | \eqn{64} SNPs are in cluster {-}, \eqn{708} SNPs are in cluster \eqn{0},
       |                              ^
Packages required but not available: 'dplyr', 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mombf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'RSQLite', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'dplyr', 'purrr', 'tibble', 'tidyr', 'lubridate',
  'testthat', 'progress'

Package suggested but not available for checking: ‘httptest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'leaflet.extras', 'nhdplusTools', 'purrr', 'tidyr',
  'elevatr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EnvStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following HTML validation problems:
gedit.html:139:6 (gedit.Rd:72): Warning: trimming empty <p>
gedit.html:139:1 (gedit.Rd:72): Warning: trimming empty <li>
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:285: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:286-293: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:378: Lost braces
   378 | \item{visible}{logical. If code{TRUE} window is drawn when
       |                                ^
Running ‘run-tests.R’ [0s/1s]
Running the tests in ‘tests/run-tests.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'plotly', 'piggyback'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'plotly', 'viridis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'broom', 'reshape2', 'plotROC', 'kableExtra', 'ggrepel',
  'cowplot', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'lubridate', 'readxl'

Package suggested but not available for checking: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘trekcolors’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'IRdisplay', 'plotly', 'repr'
Package required but not available: ‘tidyr’

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'lubridate'

Packages suggested but not available for checking:
  'testthat', 'gapminder', 'DiagrammeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'concaveman', 'purrr', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

Packages suggested but not available for checking: 'testthat', 'httptest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tidyselect', 'tibble'

Packages suggested but not available for checking: 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'msigdbr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'latex2exp', 'reshape2', 'readr', 'readxl',
  'stringr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'dplyr', 'roxyglobals', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'patchwork', 'stringr', 'tibble'

Packages suggested but not available for checking: 'ggrastr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'ggplot2', 'hal9001', 'rsample'

Packages suggested but not available for checking: 'testthat', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyselect', 'tidysmd'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'dplyr', 'tidyr', 'purrr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'nbpMatching', 'lmerTest'
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
Packages suggested but not available for checking: 'testthat', 'shinytest2'
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'devtools', 'testthat'
Running ‘runit.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'igraph', 'magick', 'mc2d', 'purrr', 'reshape2',
  'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'lubridate', 'tidyr', 'snakecase'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'car', 'ggplot2', 'olsrr', 'ggpubr', 'devtools'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Packages required but not available: 'caret', 'ggplot2', 'patchwork'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘haplo.stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rms’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'network', 'sna', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'archive', 'dplyr', 'httr2'

Packages suggested but not available for checking:
  'httptest2', 'testthat', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'daltoolbox', 'tsmp', 'dtwclust', 'rugarch', 'forecast', 'ggplot2',
  'stringr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'vctrs'

Packages suggested but not available for checking:
  'devtools', 'modeldata', 'recipes', 'roxygen2', 'testthat', 'usethis'

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:
  'dplyr', 'cowplot', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'Seurat', 'testthat', 'ggthemes', 'ggrepel', 'patchwork',
  'tidyverse', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggtree', 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘accessors.R’ [0s/1s]
  Running ‘clear.R’ [0s/1s]
  Running ‘has.key.R’ [0s/0s]
  Running ‘set.R’ [0s/1s]
Running the tests in ‘tests/accessors.R’ failed.
Complete output:
  > library(hash)
  hash-2.2.6.3 provided by Decision Patterns
  
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/clear.R’ failed.
Complete output:
  > 
  > library(hash)
  hash-2.2.6.3 provided by Decision Patterns
  
  > library( testthat )
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'forcats', 'hms', 'readr', 'tibble', 'tidyselect', 'vctrs'

Packages suggested but not available for checking: 'pillar', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'stringr', 'nloptr'

Package suggested but not available for checking: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'loo', 'rstan', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'loo', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘R2jags’

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) deff.sigma.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:35: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'mcmcsae', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'randnet', 'stringr', 'dendextend'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'dplyr', 'colourpicker'
'LazyData' is specified without a 'data' directory
Running examples in ‘hchinamap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hchinamap
> ### Title: 'hchinamap': Mapping China and Its Provinces, Municipalities and
> ###   Autonomous Regions using R and 'Highmaps'
> ### Aliases: hchinamap
> 
> ### ** Examples
> 
> library(hchinamap)
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes


Quitting from lines 50-58 [unnamed-chunk-3] (hchinamap.Rmd)
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘hchinamap.Rmd’

SUMMARY: processing the following file failed:
  ‘hchinamap.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘klaR’
Packages required but not available: 'posterior', 'bridgesampling'

Package suggested but not available for checking: ‘cmdstanr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package required but not available: ‘bigstatsr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hdm', 'caret'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) hdda.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdda.Rd:124-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdda.Rd:128-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hddc.Rd:162-164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hddc.Rd:165-168: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'easy.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'nycflights13', 'reshape2'
File ‘hdf5r/libs/hdf5r.so’:
  Found non-API call to R: ‘SETLENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdf5r.Rmd’ using rmarkdown

Quitting from lines 86-92 [unnamed-chunk-4] (hdf5r.Rmd)
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
there is no package called 'nycflights13'
--- failed re-building ‘hdf5r.Rmd’

SUMMARY: processing the following file failed:
  ‘hdf5r.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'purrr', 'tibble', 'dplyr', 'tidyselect', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'usethis', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) lasso.proj.Rd:62: Lost braces; missing escapes or markup?
    62 |     indicated using an index vector with entries in {1,...,p} or a list thereof.}
       |                                                     ^
Package required but not available: ‘Directional’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘roxygen2’
Packages required but not available: 'genlasso', 'mediation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'devtools', 'dplyr', 'testthat', 'tidyr'

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.
Packages required but not available:
  'dplyr', 'ggjoy', 'ggplot2', 'stringr', 'ggridges', 'ggpubr',
  'Hmisc', 'questionr', 'purrr', 'tibble', 'tidyr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'EstimDiagnostics', 'waldo'
Running examples in ‘HDShOP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_frontier
> ### Title: Plot the Bayesian efficient frontier (Bauder et al. 2021) and
> ###   the provided portfolios.
> ### Aliases: plot_frontier
> 
> ### ** Examples
> 
> p <- 150
> n <- 300
> gamma <- 10
> mu <- seq(0.2,-0.2, length.out=p)
> Sigma <- RandCovMtrx(p=p)
> 
> x <- t(MASS::mvrnorm(n=n , mu=mu, Sigma=Sigma))
> 
> EW_port <- rep(1/p, length=p)
> MV_shr_port <- new_MV_portfolio_weights_BDOPS21(x=x, gamma=gamma,
+                                                 b=EW_port, beta=0.05)$weights
> GMV_shr_port <- new_MV_portfolio_weights_BDOPS21(x=x, gamma=Inf, b=EW_port,
+                                                  beta=0.05)$weights
> MV_trad_port <- new_MV_portfolio_traditional(x=x, gamma=gamma)$weights
> GMV_trad_port <- new_MV_portfolio_traditional(x=x, gamma=Inf)$weights
> 
> weights.eff <- cbind(EW_port, MV_shr_port, GMV_shr_port,
+                      MV_trad_port, GMV_trad_port)
> colnames(weights.eff) <- c("EW", "MV_shr", "GMV_shr", "MV_trad", "GMV_trad")
> 
> 
> Fplot <- plot_frontier(x, weights.eff)
         portfolio.return portfolio.sd    names
EW            0.008520545   0.13397231       EW
MV_shr        0.193166386   0.12687698   MV_shr
GMV_shr      -0.004382810   0.04488442  GMV_shr
MV_trad       0.772803434   0.28199189  MV_trad
GMV_trad     -0.007044480   0.03917439 GMV_trad
Warning in sqrt(as.double(t(mu.eff) %*% Q.est.bayes %*% mu.eff) * (V.front.bayes^2 -  :
  NaNs produced
Error in loadNamespace(x) : there is no package called ‘ggplot2’
Calls: plot_frontier ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
CovShrinkBGP14    3.511  0.078   6.303
InvCovShrinkBGP16 3.359  0.090   5.732
nonlin_shrinkLW   3.399  0.047   5.315
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'purrr', 'swfscMisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'ggplot2', 'dplyr', 'tidyr', 'broom', 'tidyselect',
  'ggridges'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'nycflights13', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clock', 'dbplyr', 'dplyr', 'lubridate', 'purrr', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'srvyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'readr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'yardstick', 'broom', 'ggrepel', 'tibble', 'dplyr', 'ggplot2',
  'tidyr', 'forcats', 'recipes', 'purrr', 'dials', 'parsnip', 'tune',
  'workflows', 'modeltime'

Packages suggested but not available for checking:
  'roxygen2', 'healthyR.data', 'tidyselect', 'janitor', 'timetk',
  'plotly', 'rsample', 'kknn', 'hardhat', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'janitor', 'dplyr', 'httr2', 'stringr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'timetk', 'ggplot2', 'dplyr', 'lubridate', 'purrr',
  'stringr', 'cowplot', 'sqldf', 'plotly'

Packages suggested but not available for checking:
  'roxygen2', 'healthyR.data', 'broom', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'timetk', 'tidyr', 'dplyr', 'purrr', 'ggplot2',
  'lubridate', 'plotly', 'recipes', 'modeltime', 'cowplot', 'forcats',
  'parsnip', 'workflowsets', 'hardhat'

Packages suggested but not available for checking:
  'roxygen2', 'rsample', 'healthyR.ai', 'stringr', 'forecast',
  'tidymodels', 'tune', 'dials', 'workflows', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'healthyR', 'healthyR.data', 'healthyR.ts', 'healthyR.ai',
  'TidyDensity', 'tidyAML', 'dplyr', 'purrr', 'tibble'

Package suggested but not available for checking: ‘roxygen2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
checkRd: (-1) colByValue.Rd:20: Lost braces; missing escapes or markup?
    20 | \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:
  'plotly', 'viridis', 'ggplot2', 'dendextend', 'reshape2', 'egg'

Packages suggested but not available for checking: 'tidyselect', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'tibble'

Packages suggested but not available for checking:
  'ggpubr', 'rerddap', 'testthat', 'tidync', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sampleSelection', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘heck/libs/heck.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_PRCODE’,
    ‘SET_PRENV’, ‘SET_PRVALUE’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'dplyr', 'tidyr', 'nycflights13', 'ggplot2',
  'purrr'
'LazyData' is specified without a 'data' directory
Running examples in ‘heddlr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_template
> ### Title: Linearly combine template elements into templates
> ### Aliases: make_template
> 
> ### ** Examples
> 
> 
> # When passed vectors, make_template flattens each vector into a single
> # string and then combines its arguments from left to right
> spList <- data.frame(Species = c(unique(iris$Species), "test string"))
> make_template(
+   heddle(spList, "SPECIES CODE GWAR ", "GWAR" = Species),
+   heddle(spList, "SPECIES CODE GWAR ", "GWAR" = Species)
+ )
[1] "SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string "
> 
> # When passed variables in a dataframe, make_template collapses each column
> # in turn, then combines the output strings from left to right
> spList <- data.frame(Species = c(unique(iris$Species), "test string"))
> spList$template <- heddle(spList, "SPECIES CODE GWAR ", "GWAR" = Species)
> make_template(spList, template)
[1] "SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string "
> make_template(spList, template, template)
[1] "SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string SPECIES CODE 1 SPECIES CODE 2 SPECIES CODE 3 SPECIES CODE test string "
> 
> # When passed nested columns, heddlr collapses each cell into a string,
> # then collapses each column into a string, and then combines the outputs
> # from left to right
> make_template(tidyr::nest(spList, nested = template), nested)
Error in loadNamespace(x) : there is no package called ‘tidyr’
Calls: make_template ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘modular-reporting-with-heddlr.Rmd’ using rmarkdown

Quitting from lines 188-191 [unnamed-chunk-9] (modular-reporting-with-heddlr.Rmd)
Error: processing vignette 'modular-reporting-with-heddlr.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘modular-reporting-with-heddlr.Rmd’

SUMMARY: processing the following file failed:
  ‘modular-reporting-with-heddlr.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tibble', 'purrr', 'vctrs'

Packages suggested but not available for checking:
  'BCEA', 'flexsurv', 'optimx', 'readxl', 'rgho', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'daltoolbox', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'stringr', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggforce'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rvest', 'taxize'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'lme4', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘precrec’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'autothresholdr', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom', 'car', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'candisc', 'effects', 'reshape2', 'animation', 'mvinfluence',
  'dplyr', 'tidyr', 'ggplot2', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'readr', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) marker_h2.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:96-97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:41-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'cplm', 'DESeq2', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) glm.hermite.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:55-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:61-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:66-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) phermite.Rd:38: Lost braces; missing escapes or markup?
    38 |   {b} and \code{m} to be lower (or greater) than \code{q}.
       |   ^
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'patchwork'
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hermiter.Rmd’ using rmarkdown

Quitting from lines 69-77 [unnamed-chunk-2] (hermiter.Rmd)
Error: processing vignette 'hermiter.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘hermiter.Rmd’

SUMMARY: processing the following file failed:
  ‘hermiter.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘optimx’

Packages suggested but not available for checking:
  'autoimage', 'devtools', 'fda', 'igraph', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'flexsurv', 'ggplot2'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'huge'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'BDgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mleHetGP.Rd:57: Lost braces; missing escapes or markup?
    57 | Level \code{2} gives more details. Level {3} additionaly displays all details about initialization of hyperparameters.
       |                                          ^
checkRd: (-1) mleHetTP.Rd:61: Lost braces; missing escapes or markup?
    61 | Level \code{2} gives more details. Level {3} additionaly displays all details about initialization of hyperparameters.
       |                                          ^
checkRd: (-1) mleHomTP.Rd:76: Lost braces; missing escapes or markup?
    76 | \item \code{nit_opt}, \code{msg}: \code{counts} and {msg} returned by \code{\link[stats]{optim}}
       |                                                     ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'dplyr', 'ggplot2', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'hedgehog', 'ggExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'reshape2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'processmapR', 'dplyr', 'tidyr', 'DiagrammeR', 'petrinetR',
  'purrr', 'ggplot2', 'ggthemes', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("bittermelon")
  
  Attaching package: 'bittermelon'
  
  The following object is masked from 'package:base':
  
      which
  
  > library("hexfont")
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggimage', 'ggplot2'

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: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dendextend’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
Package required but not available: ‘genscore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'hms', 'lubridate', 'purrr', 'readr', 'rvest', 'stringr',
  'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'lubridate', 'stringr', 'usethis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'Hmisc'

Packages suggested but not available for checking:
  'car', 'Rcmdr', 'RcmdrPlugin.HH', 'microplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mice', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggnewscale', 'ggplot2', 'ggrepel', 'purrr', 'tibble',
  'tidyr', 'viridis', 'vroom'

Packages suggested but not available for checking: 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggdendro', 'ggplot2', 'viridis', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘adegenet’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) hierNet.Rd:28: Lost braces; missing escapes or markup?
    28 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |               ^
checkRd: (-1) hierNet.logistic.Rd:30: Lost braces; missing escapes or markup?
    30 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}  
       |               ^
checkRd: (-1) hierNet.logistic.Rd:63: Lost braces
    63 | \seealso{\link{predict.hierNet.logistic},link{hierNet.logistic.path}}
       |                                              ^
checkRd: (-1) hierNet.logistic.path.Rd:39: Lost braces; missing escapes or markup?
    39 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
checkRd: (-1) hierNet.path.Rd:38: Lost braces; missing escapes or markup?
    38 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
Package required but not available: ‘optimx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'dplyr', 'tibble', 'stringr', 'broom', 'tidyr', 'igraph',
  'lubridate'

Packages suggested but not available for checking:
  'ggplot2', 'gapminder', 'forecast', 'geojsonio', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rugarch', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'dplyr'
Running examples in ‘highlightHTML-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: table_id_inject
> ### Title: Table hash addition for markup
> ### Aliases: table_id_inject
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_basics.Rmd’ using rmarkdown

Quitting from lines 118-132 [symm] (the_basics.Rmd)
Error: processing vignette 'the_basics.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘the_basics.Rmd’

SUMMARY: processing the following file failed:
  ‘the_basics.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Packages required but not available: 'tibble', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘colorfulVennPlot’
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
File ‘hilbert/libs/hilbert.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr', 'reshape2'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparing_samples.Rmd’ using rmarkdown

Quitting from lines 78-86 [unnamed-chunk-4] (comparing_samples.Rmd)
Error: processing vignette 'comparing_samples.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘comparing_samples.Rmd’

--- re-building ‘identifying_effects.Rmd’ using rmarkdown

Quitting from lines 131-151 [unnamed-chunk-9] (identifying_effects.Rmd)
Error: processing vignette 'identifying_effects.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘identifying_effects.Rmd’

SUMMARY: processing the following files failed:
  ‘comparing_samples.Rmd’ ‘identifying_effects.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'haven', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggpubr', 'geiger', 'qgraph', 'FSA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'geiger'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rayshader’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'purrr', 'tidyr'

Packages suggested but not available for checking:
  'airportr', 'cowplot', 'progress', 'stringr', 'testthat', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘HDMT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

Packages suggested but not available for checking:
  'dplyr', 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pryr', 'rms'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nloptr', 'phytools', 'igraph', 'paleotree', 'geiger', 'phangorn',
  'TreeSim', 'corHMM'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'car', 'heplots', 'effects', 'lubridate'
Running examples in ‘HistData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bowley
> ### Title: Bowley's data on values of British and Irish trade, 1855-1899
> ### Aliases: Bowley
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Bowley)
> 
> # plot the data 
> with(Bowley,plot(Year, Value, type='b', lwd=2, 
+ 	ylab="Value of British and Irish Exports",
+ 	main="Bowley's example of the method of smoothing curves"))
> 
> # find moving averages
> # simpler version using stats::filter
> running <- function(x, width = 5){
+   as.vector(stats::filter(x, rep(1 / width, width), sides = 2))
+   }
> 
> mav3<-running(Bowley$Value, width=3)
> mav5<-running(Bowley$Value, width=5)
> mav9<-running(Bowley$Value, width=9)
> lines(Bowley$Year, mav3, col='blue', lty=2)
> lines(Bowley$Year, mav5, col='green3', lty=3)
> lines(Bowley$Year, mav9, col='brown', lty=4)
> 
> # add lowess smooth
> lines(lowess(Bowley), col='red', lwd=2)
> 
> # Initial version, using ggplot
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'FactoMineR', 'ggplot2', 'ggridges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clustermq', 'dplyr', 'ggplot2', 'posterior', 'rstan', 'tibble',
  'tidyr', 'tidyselect', 'trialr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'posterior', 'tibble', 'tidyr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Packages suggested but not available for checking: 'testthat', 'shinytest2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘test.R’ [0s/1s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package which this enhances but not available for checking: ‘HadoopStreaming’
Packages suggested but not available for checking: 'sna', 'bipartite'
Running examples in ‘HiveR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adj2HPD
> ### Title: Process an Adjacency Graph into a HivePlotData Object
> ### Aliases: adj2HPD
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> ### Example 1: a bipartite network
> ### Note: this first example has questionable scientific value!
> ### The purpose is to show how to troubleshoot and
> ### manipulate a HivePlotData object.
> 
> require(bipartite)
Loading required package: bipartite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘bipartite’
> data(Safariland) # This is a bipartite network
Warning in data(Safariland) : data set ‘Safariland’ not found
> 
> # You may wish to do ?Safariland or ?Safari for background
> 
> hive1 <- adj2HPD(Safariland, desc = "Safariland data set from bipartite")
Error: object 'Safariland' not found
Execution halted
Note: skipping ‘HiveR.Rmd’ due to unavailable dependencies:
  'sna', 'bipartite'
Packages required but not available:
  'ggplot2', 'ggpubr', 'dplyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'tidyr'
Packages required but not available:
  'devtools', 'tidyverse', 'dplyr', 'reshape2', 'tibble', 'tidyselect',
  'stringr', 'purrr', 'tidyr', 'readr', 'janitor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'stringr', 'usethis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'dplyr', 'stringr', 'purrr', 'tibble',
  'tidyselect', 'janitor', 'ggrepel'

Packages suggested but not available for checking:
  'mlmRev', 'lme4', 'testthat', 'car', 'qqplotr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'bayesplot', 'progress'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bayesplot’

Packages suggested but not available for checking:
  'lme4', 'ggplot2', 'mlmRev', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rvest', 'dplyr', 'janitor', 'lubridate', 'readr', 'stringr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'purrr', 'dplyr', 'ggplot2', 'viridis', 'GGally', 'ggbeeswarm',
  'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'htmlTable', 'viridis'

Packages suggested but not available for checking:
  'qreport', 'rms', 'mice', 'plotly', 'kableExtra', 'rio', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) nafracCalc.Rd:45: Lost braces
    45 |   as if code{y} were not of class \code{"multipleHmmDataSets"}.
       |             ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
Packages required but not available:
  'ggplot2', 'stringr', 'optimx', 'tmbstan'

Packages suggested but not available for checking:
  'rstan', 'testthat', 'moveHMM', 'unmarked'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘HMP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vctrs’

Packages suggested but not available for checking:
  'lubridate', 'pillar', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ecr', 'smoof'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘hms’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘NMF’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'glmmADMB'
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'readr', 'dplyr', 'tidyr', 'patchwork',
  'rvest', 'tibble', 'treemapify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'readr', 'RecordLinkage'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DiagrammeR’
Package required but not available: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'mice', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'igraph', 'readxl', 'stringr', 'mixOmics',
  'ggrepel', 'reshape2', 'tidyr'

Package suggested but not available for checking: ‘badger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘huxtable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'readr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'furrr', 'janitor', 'lubridate', 'purrr', 'rvest',
  'stringr', 'tidyr', 'usethis'

Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'RSQLite', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘endtoend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘questionr’

Packages suggested but not available for checking:
  'testthat', 'usethis', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'Hmisc', 'ggplot2'
Running examples in ‘horseshoe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HS.normal.means
> ### Title: The horseshoe prior for the sparse normal means problem
> ### Aliases: HS.normal.means
> 
> ### ** Examples
> 
> #Empirical Bayes example with 20 signals, rest is noise
> #Posterior mean for the signals is plotted
> #And variable selection is performed using the credible intervals
> #And the credible intervals are plotted
> truth <- c(rep(0, 80), rep(8, 20))
> data <-  truth + rnorm(100, 1)
> tau.hat <- HS.MMLE(data, Sigma2 = 1)
> res.HS1 <- HS.normal.means(data, method.tau = "fixed", tau = tau.hat,
+ method.sigma = "fixed", Sigma2 = 1)
[1] 1000
[1] 2000
[1] 3000
[1] 4000
[1] 5000
[1] 6000
> #Plot the posterior mean against the data (signals in blue)
> plot(data, res.HS1$BetaHat, col = c(rep("black", 80), rep("blue", 20)))
> #Find the selected betas (ideally, the last 20 are equal to 1)
> HS.var.select(res.HS1, data, method = "intervals")
  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0
 [75] 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> #Plot the credible intervals
> library(Hmisc)
Error in library(Hmisc) : there is no package called ‘Hmisc’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘horseshoe-vignette.Rmd’ using rmarkdown

Quitting from lines 13-18 [unnamed-chunk-1] (horseshoe-vignette.Rmd)
Error: processing vignette 'horseshoe-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘horseshoe-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘horseshoe-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'tidyverse', 'tibble', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'lubridate', 'ggplot2', 'ggraph'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mice', 'tidyr'

Package suggested but not available for checking: ‘miceadds’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'FactoMineR', 'ggforce', 'ggplot2', 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'shinytest2', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘mice’

Packages suggested but not available for checking: 'roxygen2', 'jomo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘colourpicker’
Packages suggested but not available for checking:
  'ggplot2', 'sampleSelection'
Packages required but not available:
  'dplyr', 'lubridate', 'ggplot2', 'imputeTS', 'purrr', 'forecast',
  'pdp'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) HPLB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘lme4’
Packages suggested but not available for checking: 'lme4', 'mice'
Note: skipping ‘Ch_analysing_longitudinal_dataI.Rnw’ due to unavailable dependencies:
  'lme4'
Note: skipping ‘Ch_analysing_longitudinal_dataII.Rnw’ due to unavailable dependencies:
  'lme4'
Note: skipping ‘Ch_missing_values.Rnw’ due to unavailable dependencies:
  'mice'
Note: skipping ‘Ch_simultaneous_inference.Rnw’ due to unavailable dependencies:
  'lme4'
Package suggested but not available for checking: ‘lme4’
Note: skipping ‘Ch_analysing_longitudinal_dataI.Rnw’ due to unavailable dependencies:
  'lme4'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sphet’

Package suggested but not available for checking: ‘splm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘npregfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpubr', 'tidyr', 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'loo', 'rstan'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking: 'optmatch', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'bayesplot'
Specified C++11: please drop specification unless essential
Running examples in ‘HTLR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gendata_FAM
> ### Title: Generate Simulated Data with Factor Analysis Model
> ### Aliases: gendata_FAM
> 
> ### ** Examples
> 
> ## feature #1: marginally related feature
> ## feature #2: marginally unrelated feature, but feature #2 is correlated with feature #1
> ## feature #3-5: marginally related features and also internally correlated
> ## feature #6-10: noise features without relationship with the y
> 
> set.seed(12345)
> n <- 100
> p <- 10
> 
> means <- rbind(
+   c(0, 1, 0),
+   c(0, 0, 0),
+   c(0, 0, 1),
+   c(0, 0, 1),
+   c(0, 0, 1)
+ ) * 2
> 
> means <- rbind(means, matrix(0, p - 5, 3))
> 
> A <- diag(1, p)
> A[1:5, 1:3] <- rbind(
+   c(1, 0, 0),
+   c(2, 1, 0),
+   c(0, 0, 1),
+   c(0, 0, 1),
+   c(0, 0, 1)
+ )
> 
> dat <- gendata_FAM(n, means, A, sd_g = 0.5, stdx = TRUE)
> ggplot2::qplot(dat$y, bins = 6)
Error in loadNamespace(x) : there is no package called ‘ggplot2’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'lubridate', 'progress', 'rvest', 'stringr', 'tibble',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'testthat', 'Hmisc', 'lubridate', 'tibble', 'purrr', 'tidyselect',
  'tidyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘htmltools/libs/htmltools.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'caret', 'tune', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘HTSFilter’
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'readr', 'tibble', 'lubridate',
  'stringr', 'readxl', 'RSQLite', 'shinyFiles'

Packages suggested but not available for checking: 'openair', 'editData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'stringr', 'dplyr', 'tidyr', 'ggplot2', 'DESeq2',
  'phyloseq'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'ggplot2'

Packages suggested but not available for checking:
  'EnvStats', 'stringr', 'viridis', 'cowplot', 'ggrepel', 'dplyr',
  'forcats', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httptest’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(httptest)
  Error in library(httptest) : there is no package called 'httptest'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘httpcache.Rmd’ using rmarkdown

Quitting from lines 91-92 [unnamed-chunk-6] (httpcache.Rmd)
Error: processing vignette 'httpcache.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘httpcache.Rmd’

SUMMARY: processing the following file failed:
  ‘httpcache.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Specified C++14: please drop specification unless essential
File ‘httpgd/libs/httpgd.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘pryr’

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Packages required but not available: 'httr2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘vctrs’

Packages suggested but not available for checking:
  'bench', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggraph', 'igraph', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'readr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'Hmisc', 'lubridate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘janitor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'magick', 'cowplot', 'ggplot2', 'dplyr', 'tidyr', 'tibble', 'purrr'

Packages suggested but not available for checking: 'gsheet', 'inti'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘lubridate’

Packages suggested but not available for checking: 'testthat', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘dplyr’
checkRd: (-1) CalcROC.Rd:47: Lost braces
    47 | The accuracy of the classifier is the mean value of dQuote{(optSn, optSp)} for two-class problem and the mean value of \dQuote{(optSn, optSp,optS3)} for three-class problem.
       |                                                           ^
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'reshape2', 'rstan', 'cowplot', 'Hmisc', 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggmap', 'ggplot2', 'lubridate', 'purrr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘hurricaneexposuredata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bench’
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'Hmisc', 'nycflights13', 'ggplot2', 'readr',
  'tibble', 'tidyr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'stringr', 'tidyselect'

Packages suggested but not available for checking:
  'AER', 'broom', 'broom.mixed', 'devtools', 'dplyr', 'ftExtra',
  'ggplot2', 'lme4', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'ggplot2', 'tidyr', 'reshape2', 'ggforce',
  'gganimate', 'markovchain'

Packages suggested but not available for checking:
  'testthat', 'plotly', 'patchwork', 'Hmisc', 'installr', 'skimr',
  'tibble', 'devtools', 'tidyverse', 'DataExplorer', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bridgesampling', 'rstan', 'updog'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spatsoc’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘microViz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'nnfor', 'WaveletArima'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httr2’

Packages suggested but not available for checking:
  'testthat', 'stringr', 'devtools', 'pkgdown', 'roxygen2',
  'shiny.i18n', 'lubridate', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hyd1d’

Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'roxygen2', 'testthat', 'shiny.i18n',
  'leaflet.extras', 'leaflet.esri', 'pangaear', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Packages required but not available:
  'ggplot2', 'purrr', 'reshape2', 'tibble'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'nhdplusTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggpmisc', 'ggplot2', 'lubridate', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplyr’
Running examples in ‘hydrostats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flood.length.max
> ### Title: Calculates the maximum flood length in a time series.
> ### Aliases: flood.length.max
> 
> ### ** Examples
> 
> 
> data(Cooper)
> Cooper<-ts.format(Cooper)
> 
> flood.length.max(Cooper, threshold = 50000, ind.days = 5)
  max.duration
1           40
> 
> # Return annual maximum flood length based on calendar year using ddply (from plyr package) 
> require(plyr)
Loading required package: plyr
> Cooper$Year=format(Cooper$Date, format="%Y")
> ddply(Cooper, .(Year), flood.length.max, threshold = 50000)
   Year max.duration
1  1967            0
2  1968           13
3  1969            0
4  1970            0
5  1971           10
6  1972            6
7  1973           17
8  1974           40
9  1975            2
10 1976           21
11 1977           19
12 1978            0
13 1979            8
14 1980            1
15 1981            3
16 1982            0
17 1983           10
18 1984            0
19 1985            0
20 1986            7
21 1987            0
> 
> require(dplyr)
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘dplyr’
> Cooper %>%
+ dplyr::group_by(Year) %>%
+ dplyr::do(flood.length.max(., threshold = 50000))
Error in Cooper %>% dplyr::group_by(Year) %>% dplyr::do(flood.length.max(.,  : 
  could not find function "%>%"
Execution halted
Packages required but not available:
  'ggplot2', 'plotly', 'lubridate', 'readxl', 'reshape2', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'lubridate', 'readxl', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'EnvStats', 'lubridate', 'tibble'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'nloptr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'stringr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'matlib', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'testthat', 'dplyr'

Packages suggested but not available for checking: 'devtools', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'progress', 'ggplot2', 'purrr', 'dplyr', 'caret'

Packages suggested but not available for checking: 'magick', 'alphahull'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'ggrepel', 'lubridate', 'patchwork',
  'purrr', 'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'beepr', 'leaflet.extras', 'plotly', 'shinyFiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking:
  'testthat', 'mockery', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'sjPlot'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

Packages suggested but not available for checking: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'incidence2', 'ciTools', 'dplyr', 'tibble', 'tidyr', 'vctrs',
  'ggplot2', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FrF2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'dplyr', 'tidyr', 'dplR', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'ggplot2', 'cowplot'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'ggplot2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘a_intro.Rmd’ using rmarkdown
--- finished re-building ‘a_intro.Rmd’

--- re-building ‘b_analysis.Rmd’ using rmarkdown

Quitting from lines 37-40 [preview_liquor] (b_analysis.Rmd)
Error: processing vignette 'b_analysis.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘b_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘b_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'Hmisc', 'vcdExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'dplyr', 'reshape2', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'ggpubr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘real_data.Rmd’ using rmarkdown

Quitting from lines 65-77 [size_plot] (real_data.Rmd)
Error: processing vignette 'real_data.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘real_data.Rmd’

--- re-building ‘simulation.Rmd’ using rmarkdown

Quitting from lines 113-125 [size_plot] (simulation.Rmd)
Error: processing vignette 'simulation.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘simulation.Rmd’

SUMMARY: processing the following files failed:
  ‘real_data.Rmd’ ‘simulation.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dslabs', 'ggplot2', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'tidyverse', 'kableExtra', 'caret', 'reshape2', 'lubridate',
  'patchwork', 'ggrepel', 'GGally', 'ggfortify', 'cowplot',
  'gutenbergr', 'tidytext', 'Lahman', 'waldo', 'rvest', 'usethis',
  'vdiffr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ggplot2', 'SparkR'
Packages required but not available: 'readr', 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'ggfortify', 'magick', 'gganimate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'DALEX', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) setServerLogLevel.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) betaS1lr.Rd:28: Lost braces; missing escapes or markup?
    28 |  \item{Rm1U}{matrix R^{-1}U (see reference).}
       |                       ^
checkRd: (-1) lrsmoother.Rd:32: Lost braces; missing escapes or markup?
    32 |   R^{-1}U (see reference) and \link{smoothCon} for the definition of smoothobject}
       |     ^
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'tidyselect'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'dplyr', 'ggplot2', 'plotROC', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'ggplot2', 'igraph', 'reshape2', 'mc2d'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'purrr', 'latex2exp', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'RLRsim', 'testthat'

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
Running examples in ‘ICCbin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iccbin
> ### Title: Estimates Intracluster Correlation coefficients (ICC) and it's
> ###   confidence intervals (CI)
> ### Aliases: iccbin
> 
> ### ** Examples
> 
> bccdata <- rcbin(prop = .4, prvar = .2, noc = 30, csize = 20, csvar = .2, rho = .2)
> iccbin(cid = cid, y = y, data = bccdata)
Warning in iccbin(cid = cid, y = y, data = bccdata) :
  One or Both of 'Zou and Donner's Modified Wald' Confidence Limits Fell Outside of [0, 1]
Error: Package 'lme4' is needed for methods 'lin' and 'sim'. Please install it.
Execution halted
Packages required but not available: 'glmmTMB', 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'tidyselect', 'tibble'

Packages suggested but not available for checking: 'testthat', 'rvest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'icd'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'graphite', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pillar', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Packages required but not available:
  'ggplot2', 'plotly', 'ggrepel', 'ggpubr', 'ggdendro', 'Hmisc',
  'progress', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mixAK', 'frailtypack', 'dynsurv'
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'purrr', 'tidyverse', 'readxl', 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Bpa.Rd:39-40: Lost braces
    39 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) Fpa.Rd:42-43: Lost braces
    42 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) icesRound.Rd:64-65: Lost braces
    64 | \doi{10.17895/ices.pub.3038}{\emph{ICES Advice Technical
       |                             ^
checkRd: (-1) mohn.Rd:71-72: Lost braces
    71 | \doi{10.17895/ices.pub.5997}{\emph{ICES Scientific Reports
       |                             ^
Packages required but not available: 'leaflet.extras', 'lubridate', 'rvest'

Packages suggested but not available for checking:
  'reshape2', 'plotly', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sqldf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'purrr', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rugarch', 'car', 'coefplot', 'forecast', 'lubridate', 'openair',
  'papeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tsutils’

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rvest', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) ic.ranks.Rd:46: Lost braces; missing escapes or markup?
    46 | \item{n_adjust}{an integer-valued entry for advanced control over the lower- or upper-bound algorithms. When the "adjustL" parameter is TRUE, the new value of n_adjust is chosen automatically as the best adjustment on the lower affine bound of the chi-square quantiles according to the data. If adjustU is TRUE, then n_adjust contains the point at which the upper affine bound is tangent on the chi-square quantiles. Possible values {1,...,n-1}. If both adjustL and adjustU variables are left FALSE, then the default choice is that the lower affine bound passes between the chi-square quantiles at 1 and n-1 degrees of freedom, and the upper affine bound is tangent on n-1.}
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘icrf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: survplot
> ### Title: 'Plotting individual survival curves'
> ### Aliases: survplot
> 
> ### ** Examples
> 
> # rats data example.
> # Note that this is a toy example. Use a larger ntree and nfold in practice.
> data(rat2)
> ## Don't show: 
>  set.seed(1)
>  rats.icrf <-
+    icrf(~ dose.lvl + weight + male + cage.no, data = rat2,
+         data.type = "currentstatus", currentstatus.label = c("survtime", "tumor"),
+         returnBest = TRUE, ntree=2, nfold=2)

Forest loop 1 out of 2 folds
Tree 1 2 
   IMSE1 (OOB, non-OOB) = (0.131, 0.085), IMSE2 = (0.252, 0.193)
Forest loop 2 out of 2 folds
Tree 1 2 
   IMSE1 (OOB, non-OOB) = (0.134, 0.079), IMSE2 = (0.268, 0.193)
>  survplot(rats.icrf, c(1,3,5))
Error in loadNamespace(x) : there is no package called ‘ggplot2’
Calls: survplot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘icr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: krippalpha
> ### Title: Krippendorff's alpha
> ### Aliases: krippalpha
> 
> ### ** Examples
> 
> data(codings)
> 
> # compute alpha, without uncertainty estimates
> krippalpha(codings)

 Krippendorff's alpha 

 alpha coders units   level
 0.743      4    12 nominal

 Bootstrapped alpha
 Alpha Std. Error 2.5 % 97.5 % Boot. technique Bootstraps
    NA         NA    NA     NA    Krippendorff         NA
    NA         NA    NA     NA   nonparametric         NA

 P(alpha > alpha_min):
 alpha_min krippendorff nonparametric
      0.90           NA            NA
      0.80           NA            NA
      0.70           NA            NA
      0.67           NA            NA
      0.60           NA            NA
      0.50           NA            NA
> 
> # additionally compute bootstrapped uncertainty estimates for alpha
> alpha <- krippalpha(codings, metric = "nominal", bootstrap = TRUE, bootnp = TRUE)
> alpha

 Krippendorff's alpha 

 alpha coders units   level
 0.743      4    12 nominal

 Bootstrapped alpha
 Alpha Std. Error 2.5 % 97.5 % Boot. technique Bootstraps
  0.72      0.074 0.562   0.85    Krippendorff      20000
  0.73      0.146 0.417   1.00   nonparametric       1000

 P(alpha > alpha_min):
 alpha_min krippendorff nonparametric
      0.90        0.004         0.126
      0.80        0.133         0.350
      0.70        0.640         0.607
      0.67        0.739         0.683
      0.60        0.940         0.822
      0.50        0.996         0.932
> 
> # plot bootstrapped alphas
> plot(alpha)
> 
> # alternatively, use ggplot2
> df <- plot(alpha, return_data = TRUE)
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: 'ggplot2', 'GGally', 'heplots'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ICSClust', 'testthat'
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) data.Rd:7: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:9: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## load dependencies
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggnewscale', 'ggplot2', 'metR', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_ICvectorfields.Rmd’ using rmarkdown

Quitting from lines 19-25 [setup] (Using_ICvectorfields.Rmd)
Error: processing vignette 'Using_ICvectorfields.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Using_ICvectorfields.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_ICvectorfields.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'purrr', 'stringr'

Packages suggested but not available for checking: 'tidyr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nrba', 'dplyr', 'tibble', 'srvyr', 'haven', 'readr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'pillar', 'purrr'

Packages suggested but not available for checking:
  'dplyr', 'shinytest', 'shinytest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'tidyr', 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readxl', 'tibble', 'ggimage', 'ggpubr', 'ggplot2', 'ggtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'dfidx'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'sqldf', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rggobi’
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'FRK'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'ggpubr', 'ggtree', 'phytools', 'treeio', 'kableExtra',
  'badger'

VignetteBuilder packages required for checking but not installed:
  'kableExtra', 'badger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘usethis’

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:
  'egg', 'ggplot2', 'igraph', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'viridis', 'purrr', 'furrr', 'stringr', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'testthat', 'pkgnet', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'animation', 'ggrepel'

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'igraph', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IDSL.IPA', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readxl’
Package required but not available: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IDSL.IPA', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IDSL.IPA', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IDSL.IPA', 'IDSL.UFA', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'rvest', 'lubridate'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Southeast-USA-Engineering-Weather-Map.Rmd’ using rmarkdown

Quitting from lines 23-95 [unnamed-chunk-1] (Southeast-USA-Engineering-Weather-Map.Rmd)
Error: processing vignette 'Southeast-USA-Engineering-Weather-Map.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building ‘Southeast-USA-Engineering-Weather-Map.Rmd’

--- re-building ‘USA-Engineering-Weather-Map.Rmd’ using rmarkdown

Quitting from lines 23-93 [unnamed-chunk-1] (USA-Engineering-Weather-Map.Rmd)
Error: processing vignette 'USA-Engineering-Weather-Map.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building ‘USA-Engineering-Weather-Map.Rmd’

SUMMARY: processing the following files failed:
  ‘Southeast-USA-Engineering-Weather-Map.Rmd’
  ‘USA-Engineering-Weather-Map.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'readxl', 'lubridate'

Package suggested but not available for checking: ‘rando’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rvest', 'ggplot2', 'qdap', 'lubridate', 'snakecase', 'dplyr',
  'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building ‘East-Palestine-Ohio_Norfolk-Southern-Train-32N-Cargo_Chemical-Databases.Rmd’ using rmarkdown
--- finished re-building ‘East-Palestine-Ohio_Norfolk-Southern-Train-32N-Cargo_Chemical-Databases.Rmd’

--- re-building ‘Tables_with_Notes.Rmd’ using rmarkdown
--- finished re-building ‘Tables_with_Notes.Rmd’

--- re-building ‘US_Locations_Fukushima_Radiation_Sampled_2011.Rmd’ using rmarkdown

Quitting from lines 23-60 [unnamed-chunk-1] (US_Locations_Fukushima_Radiation_Sampled_2011.Rmd)
Error: processing vignette 'US_Locations_Fukushima_Radiation_Sampled_2011.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building ‘US_Locations_Fukushima_Radiation_Sampled_2011.Rmd’

--- re-building ‘View-PDF-table.Rmd’ using rmarkdown
--- finished re-building ‘View-PDF-table.Rmd’

SUMMARY: processing the following file failed:
  ‘US_Locations_Fukushima_Radiation_Sampled_2011.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'ggpubr', 'sjmisc', 'lubridate', 'matlab2r'

Packages suggested but not available for checking:
  'sampler', 'rando', 'linguisticsdown', 'hydraulics', 'ie2misc',
  'tibble', 'opencpu'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggwordcloud’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Analysis-using-tm-vignette.Rmd’ using rmarkdown

Quitting from lines 23-142 [unnamed-chunk-1] (Analysis-using-tm-vignette.Rmd)
Error: processing vignette 'Analysis-using-tm-vignette.Rmd' failed with diagnostics:
could not find function "ggwordcloud"
--- failed re-building ‘Analysis-using-tm-vignette.Rmd’

--- re-building ‘View-PDFs-vignette.Rmd’ using rmarkdown
--- finished re-building ‘View-PDFs-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Analysis-using-tm-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘IFCdata’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readxl', 'rvest', 'tidyr'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

Packages suggested but not available for checking:
  'forecast', 'keras', 'lubridate', 'tensorflow', 'tibble', 'timetk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘haplo.stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MBESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'stringr', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vctrs’

Packages suggested but not available for checking:
  'testthat', 'tibble', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'hms', 'lubridate', 'patchwork',
  'tibble', 'tidyr', 'plotly'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'
Running examples in ‘igoR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: igo_dyadic
> ### Title: Extract the Joint Membership of a pair of Countries across IGOs.
> ### Aliases: igo_dyadic
> 
> ### ** Examples
> 
> usa_esp <- igo_dyadic("USA", "Spain")
> nrow(usa_esp)
[1] 199
> ncol(usa_esp)
[1] 546
> 
> dplyr::tibble(usa_esp)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘igoR.Rmd’ using rmarkdown

Quitting from lines 84-89 [setup] (igoR.Rmd)
Error: processing vignette 'igoR.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘igoR.Rmd’

--- re-building ‘mapping.Rmd’ using rmarkdown
--- finished re-building ‘mapping.Rmd’

SUMMARY: processing the following file failed:
  ‘igoR.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'shinyFiles', 'purrr', 'stringr', 'lubridate', 'tibble', 'dplyr',
  'tidyr', 'fuzzyjoin', 'rio', 'arrow', 'feather', 'haven', 'readxl',
  'readODS', 'Hmisc', 'skimr', 'ggformula'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'ggplot2', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vctrs’

Packages suggested but not available for checking:
  'decor', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'metR', 'ggplot2', 'testthat'
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("igrf")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘igrf.Rmd’ using rmarkdown

Quitting from lines 55-85 [unnamed-chunk-3] (igrf.Rmd)
Error: processing vignette 'igrf.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘igrf.Rmd’

SUMMARY: processing the following file failed:
  ‘igrf.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'factoextra', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggdendro’

Packages suggested but not available for checking:
  'testthat', 'reshape2', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'readr', 'tibble', 'tidytext', 'bib2df',
  'stringr', 'usethis', 'gender'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'readxl', 'rvest', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) simHawkes1a.Rd:35: Lost braces; missing escapes or markup?
    35 | distribution; 'd${dis}' gives the density function \eqn{g(\cdot)}.}
       |                  ^
Packages required but not available: 'caret', 'stringr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘R2jags’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'readr', 'strex', 'stringr'

Packages suggested but not available for checking:
  'mockery', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fda.usc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) define_target_function.Rd:41: Lost braces; missing escapes or markup?
    41 | be done either as a single vector of values (e.g. `function(x) { ... }`), or individual inputs for each parameter
       |                                                                ^
checkRd: (-1) define_target_function.Rd:42: Lost braces; missing escapes or markup?
    42 | (e.g. `function(x1, x2) { ... }`). If a single vector is used, all parameters will be passed to the target function as
       |                         ^
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘magick’
Package suggested but not available for checking: ‘magick’
checkRd: (-1) image_contour_detector.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_contour_detector.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘magick’
Running examples in ‘image.CornerDetectionF9-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: image_detect_corners
> ### Title: Find Corners in Digital Images with FAST-9.
> ### Aliases: image_detect_corners
> 
> ### ** Examples
> 
> library(pixmap)
> imagelocation <- system.file("extdata", "chairs.pgm", package="image.CornerDetectionF9")
> image   <- read.pnm(file = imagelocation, cellres = 1)
Read 262144 items
> x       <- image@grey * 255
> corners <- image_detect_corners(x, 80)
> plot(image)
> points(corners$x, corners$y, col = "red", pch = 20, lwd = 0.5)
> 
> ##
> ## image_detect_corners expects a matrix as input
> ##  if you have a jpg/png/... convert it to pgm first or take the r/g/b channel
> library(magick)
Error in library(magick) : there is no package called ‘magick’
Execution halted
Package suggested but not available for checking: ‘magick’
Packages required but not available:
  'dae', 'ggplot2', 'readxl', 'Hmisc', 'GGally'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘magick’
checkRd: (-1) image_fhog.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_fhog.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_surf.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Running examples in ‘image.dlib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: image_fhog
> ### Title: HOG (Histogram Of Gradients) feature extraction
> ### Aliases: image_fhog
> 
> ### ** Examples
> 
> library(magick)
Error in library(magick) : there is no package called ‘magick’
Execution halted
Package required but not available: ‘magick’

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'mockery', 'furrr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘magick’
Specified C++11: please drop specification unless essential
Running examples in ‘image.libfacedetection-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: image_detect_faces
> ### Title: Detect faces in images using the libfacedetection CNN
> ### Aliases: image_detect_faces
> 
> ### ** Examples
> 
> library(magick)
Error in library(magick) : there is no package called ‘magick’
Execution halted
Package suggested but not available for checking: ‘magick’
checkRd: (-1) image_line_segment_detector.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:66-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) image_line_segment_detector.Rd:73-76: Lost braces in \itemize; \value handles \item{}{} directly
Running examples in ‘image.LineSegmentDetector-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: image_line_segment_detector
> ### Title: Line Segments Detection (LSD) in an image
> ### Aliases: image_line_segment_detector
> 
> ### ** Examples
> 
> library(pixmap)
> imagelocation <- system.file("extdata", "chairs.pgm", package="image.LineSegmentDetector")
> image <- read.pnm(file = imagelocation, cellres = 1)
Read 262144 items
> x <- image@grey * 255
> 
> linesegments <- image_line_segment_detector(x)
> linesegments
Line Segment Detector
  found 700 line segments
> plot(image)
> plot(linesegments, add = TRUE, col = "red")
> 
> 
> ##
> ## image_line_segment_detector expects a matrix as input
> ##  if you have a jpg/png/... convert it to pgm first or take the r/g/b channel
> library(magick)
Error in library(magick) : there is no package called ‘magick’
Execution halted
Package suggested but not available for checking: ‘magick’
Specified C++11: please drop specification unless essential
Running examples in ‘image.Otsu-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: image_otsu
> ### Title: Image segmentation using Otsu
> ### Aliases: image_otsu
> 
> ### ** Examples
> 
> library(magick)
Error in library(magick) : there is no package called ‘magick’
Execution halted
Package required but not available: ‘imager’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'purrr', 'igraph'

Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'testthat', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'keras', 'magick', 'purrr', 'tibble', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'distributions3', 'dplyr', 'lubridate', 'tibble'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'smotefamily', 'C50'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'tibble', 'janitor'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IsingSampler', 'igraph', 'qgraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'MBESS'

Package suggested but not available for checking: ‘mediation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'caret', 'tidyverse', 'ggpubr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'magick', 'ggplot2', 'usethis', 'pillar', 'rtweet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixtools', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'bench', 'caret', 'keras', 'mlr', 'patchwork', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'igraph', 'clusterProfiler', 'DOSE', 'dplyr', 'org.Hs.eg.db',
  'purrr', 'ggplot2', 'ggheatmap', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘lme4’
Packages required but not available: 'dplyr', 'caret', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'dtplyr', 'patchwork', 'factoextra', 'UpSetR',
  'ggrepel', 'reshape2', 'readxl', 'airr', 'ggseqlogo', 'ggalluvial',
  'ggpubr', 'purrr', 'readr', 'stringr', 'tibble', 'tidyselect',
  'tidyr', 'igraph', 'phangorn', 'ggraph'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'stringr', 'reshape2', 'ggplot2', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rvest', 'devtools'
checkRd: (-1) stringCSSRule.Rd:22: Lost braces
    22 | using the {{placeholder}} convention.
       |           ^
checkRd: (-1) stringTemplate.Rd:23: Lost braces
    23 | placeholders are marked using the {{placeholder}} convention.
       |                                   ^
checkRd: (-1) stringTemplate.Rd:12: Lost braces
    12 | {{placeholder}} format.}
       | ^
Package required but not available: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'tibble', 'dplyr', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'lvmisc', 'pillar', 'purrr', 'stringr', 'tibble',
  'toOrdinal', 'vroom'

Packages suggested but not available for checking: 'accdata', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'dbplyr', 'tidyselect'

Packages suggested but not available for checking:
  'Lahman', 'lubridate', 'odbc', 'nycflights13', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplyr’
'LazyData' is specified without a 'data' directory
Running examples in ‘importar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: import
> ### Title: This function imports/loads packages as in 'Python', i.e.,
> ###   "import package as alias"
> ### Aliases: import
> 
> ### ** Examples
> 
> import(dplyr, d)
Error in library(package., character.only = TRUE) : 
  there is no package called ‘dplyr’
Calls: import -> <Anonymous> -> withCallingHandlers -> library
Execution halted
Packages required but not available: 'Hmisc', 'readxl', 'haven'

Package suggested but not available for checking: ‘compareGroups’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'haven', 'rio'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'tidyr', 'cowplot', 'ggplot2', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
checkRd: (-1) imptree_params.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imptree_params.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.imptree.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.imptree.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (C) 2018  Paul Fink
  > #
  > # This file is part of imptree.
  > #
  > # imptree is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 2 of the License, or
  > # (at your option) any later version.
  > #
  > # imptree is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with imptree.  If not, see <https://www.gnu.org/licenses/>.
  > 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘parsnip’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'tibble', 'dplyr', 'tidyr', 'stringr', 'purrr', 'broom'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mice', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'testthat', 'caret', 'Cubist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forecast', 'ggplot2', 'imputeTS', 'reshape2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggtext', 'forecast'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'tsibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'caret', 'ggplot2', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) kmpp.Rd:27: Lost braces
    27 |   \item{call}{a string containing the matched function call that generates this sQuote{inaparc} object.}
       |                                                                                       ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tibble'
Running examples in ‘incase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: if_case
> ### Title: Pipe-friendly vectorized if
> ### Aliases: if_case
> 
> ### ** Examples
> 
> x <- c(1, 2, 5, NA)
> 
> # if_case() produces the same output as dplyr::if_else()
> if_case(x > 3, "high", "low", "missing")
[1] "low"     "low"     "high"    "missing"
> dplyr::if_else(x > 3, "high", "low", "missing")
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘genefilter’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'dtwclust', 'dendextend', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'pillar', 'tibble', 'tidyr', 'dplyr', 'tidyselect', 'vctrs'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CDMConnector', 'dbplyr', 'dplyr', 'ggplot2', 'omopgenerics',
  'lubridate', 'purrr', 'stringr', 'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'RPostgres', 'odbc', 'Hmisc', 'testthat', 'PaRe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘backbone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'suncalc', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'tibble'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phangorn’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cobalt’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lubridate', 'RcppBDT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘indexnumr.Rmd’ using rmarkdown

Quitting from lines 16-21 [setup] (indexnumr.Rmd)
Error: processing vignette 'indexnumr.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘indexnumr.Rmd’

SUMMARY: processing the following file failed:
  ‘indexnumr.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

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.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'SixSigma'

Packages suggested but not available for checking:
  'tibble', 'stringr', 'purrr', 'janitor', 'patchwork', 'forcats',
  'broom', 'viridis', 'car', 'qicharts2', 'ggforce', 'ggraph',
  'tidygraph', 'igraph', 'RcmdrMisc', 'gt', 'skimr', 'ggtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'tibbletime'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'tibble', 'ggplot2', 'reshape2', 'tidytree', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'dplyr', 'ggpubr', 'purrr', 'iNEXT.3D'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'iNEXT.3D', 'tibble', 'dplyr', 'tidytree', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'testthat', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggnetwork', 'ggplot2', 'ggraph', 'patchwork', 'progress',
  'purrr'

Packages suggested but not available for checking:
  'igraph', 'precrec', 'testthat', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'patchwork', 'purrr', 'tibble', 'tidyr',
  'vctrs'

Packages suggested but not available for checking:
  'devtools', 'nycflights13', 'parsnip', 'stringr', 'testthat',
  'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘minfi’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'readxl', 'tidyr', 'ggplot2', 'GGally', 'network'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'ggrepel'

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: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'janitor', 'ggplot2'

Packages suggested but not available for checking:
  'Hmisc', 'readr', 'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'httptest'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'purrr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

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: 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'ggplot2', 'patchwork', 'purrr', 'tidyr', 'preferably', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘gurobi’
Package required but not available: ‘nloptr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rNOMADS’
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
Packages required but not available: 'spaMM', 'blackbox', 'viridis'

Packages suggested but not available for checking:
  'testthat', 'caret', 'xLLiM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'DALEX', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library (testthat);
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'lubridate', 'metR', 'purrr',
  'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'kableExtra', 'survminer', 'lme4', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Packages required but not available: 'fmesher', 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'ggmap', 'ggplot2', 'INLA', 'patchwork', 'tidyterra', 'testthat',
  'tidyr', 'DiagrammeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'ggplot2'

Packages suggested but not available for checking:
  'INLA', 'JMbayes2', 'rstanarm', 'frailtypack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fmesher’

Packages suggested but not available for checking:
  'INLA', 'inlabru', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'connectapi', 'pkgdown', 'roxygen2'
Packages suggested but not available for checking:
  'archive', 'arrow', 'connectapi', 'dataRetrieval', 'DiagrammeR',
  'dm', 'pkgdown', 'roxygen2'
Running examples in ‘inldata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract_archive
> ### Title: Extract Archive Contents
> ### Aliases: extract_archive
> ### Keywords: internal
> 
> ### ** Examples
> 
> files <- system.file("extdata", "test.zip", package = "inldata") |>
+   extract_archive()
Error: Extracting contents of an archive requires the 'archive' package
Execution halted
Packages suggested but not available for checking:
  'connectapi', 'kableExtra', 'magick', 'pkgdown'
Running examples in ‘inlpubs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_webpages
> ### Title: Create Author and Publication Webpages
> ### Aliases: make_webpages
> ### Keywords: internal
> 
> ### ** Examples
> 
> destdir <- tempfile("")
> make_webpages(
+   authors = inlpubs::authors,
+   pubs = inlpubs::pubs,
+   destdir = destdir,
+   quiet = TRUE
+ )
Error in loadNamespace(x) : there is no package called ‘kableExtra’
Calls: make_webpages ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'GGally', 'keras', 'lime', 'luz', 'plotly', 'tensorflow', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'purrr', 'dplyr', 'nycflights13'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 235-249 [unnamed-chunk-11] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'nycflights13'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘entropart’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘suncalc’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'ggpubr', 'patchwork', 'purrr',
  'readxl', 'tidyr'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘taxize’

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'tibble', 'dplyr', 'stringr', 'tidyselect', 'purrr'

Packages suggested but not available for checking:
  'tidyverse', 'lubridate', 'kableExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFactor', 'blavaan', 'blme', 'brms', 'broom',
  'car', 'cgam', 'cplm', 'epiR', 'feisr', 'fungible', 'gamm4',
  'geepack', 'glmmTMB', 'gmnl', 'gt', 'httptest2', 'httr2', 'ivreg',
  'lavaSearch2', 'lme4', 'lmerTest', 'logistf', 'logitr', 'merTools',
  'metaBMA', 'metaplus', 'mice', 'mlogit', 'mmrm', 'nestedLogit',
  'panelr', 'parsnip', 'pbkrtest', 'PROreg', 'rms', 'robustlmm',
  'rstanarm', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'InterVA5'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggfittext', 'progress', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'brms', 'dplyr', 'ggplot2', 'lme4', 'modelr', 'plotly', 'purrr',
  'readxl', 'tidybayes', 'tidyr', 'vroom'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 20-24 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'testthat', 'mockery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Malformed Title field: should not end in a period.
Packages required but not available:
  'ciTools', 'DHARMa', 'dplyr', 'ggplot2', 'lubridate', 'patchwork',
  'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'intamap', 'automap', 'spcosa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘automap’

Package suggested but not available for checking: ‘psgp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'DiagrammeR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'pointblank', 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'lubridate', 'tidyr', 'tibble', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'igraph', 'intergraph', 'sna', 'viridis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'chngpt', 'tidyr', 'ggbeeswarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'pryr', 'stringr'

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'jtools', 'tibble'

Packages suggested but not available for checking:
  'broom', 'cowplot', 'ggstance', 'huxtable', 'lme4', 'margins',
  'testthat', 'vdiffr'

Packages which this enhances but not available for checking:
  'brms', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'ggrepel', 'readr', 'readxl', 'FactoMineR',
  'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'ggplot2', 'DescTools', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggplotify', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'network', 'igraph'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'tibble'

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: ‘reshape2’

Packages suggested but not available for checking: 'kableExtra', 'testthat'

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: 'intergraph', 'igraph', 'network'

Packages suggested but not available for checking:
  'TDA', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'arm', 'dplyr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'stringr'
Note: skipping ‘partDeriv.Rnw’ due to unavailable dependencies:
  'ggplot2', 'stringr'
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'ggplot2', 'ggbeeswarm', 'patchwork',
  'aplot', 'moonBook'

Package suggested but not available for checking: ‘PairedData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RSQLite', 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘NMF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
checkRd: (-1) remit.Rd:32: Lost braces
    32 | A data set to replicate the findings of Escrib\`{a}-Folch,
       |                                                 ^
checkRd: (-1) remit.Rd:38: Lost braces
    38 | Escrib\`{a}-Folch, A., Meseguer, C. and Wright, J. (2018), Remittances and Protest in Dictatorships. American Journal of Political Science, 62: 889-904. \doi{10.1111/ajps.12382}
       |         ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘post-double-selection.Rmd’ using rmarkdown

Quitting from lines 78-90 [coefplot] (post-double-selection.Rmd)
Error: processing vignette 'post-double-selection.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building ‘post-double-selection.Rmd’

SUMMARY: processing the following file failed:
  ‘post-double-selection.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘readxl’

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) interval-internal.Rd:40: Lost braces
    40 | \item{dqfunc}{function, density of the results of the quantile function, e.g., function(x){dnorm(qnorm(x))} (used for 'general' scores, 
       |                                                                                           ^
Packages required but not available:
  'clinUtils', 'cowplot', 'ggplot2', 'ggrepel', 'reshape2'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'tibble', 'lme4', 'FactoMineR', 'purrr',
  'stringr', 'googlesheets4'

Package suggested but not available for checking: ‘gsheet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'stringr', 'mice', 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NMF', 'InterSIM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'patchwork', 'reshape2'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'latex2exp', '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.
Specified C++11: please drop specification unless essential
checkRd: (-1) cox_cure_net.Rd:132: Lost braces
   132 | \code{surv_lambda} (or code{cure_lambda}) that produces all-zero
       |                            ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'ggplot2', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Inventorymodel-package.Rd:34: Lost braces
    34 | M.G. Fiestras-Janeiro, I. García-Jurado, A. Meca, M.A. Mosquera (2015). Cooperation on capacitated inventory situations with fixed holding costs. emph{European Journal of Operational Research}, \bold{241}(3), 719--726.
       |                                                                                                                                                       ^
Packages suggested but not available for checking: 'tibble', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'igraph'
Running examples in ‘invertiforms-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DoubleCenter
> ### Title: Construct and use DoubleCenter transformations
> ### Aliases: DoubleCenter transform,DoubleCenter,sparseMatrix-method
> ###   inverse_transform,DoubleCenter,sparseLRMatrix-method
> ###   inverse_transform,DoubleCenter,vsp_fa-method
> 
> ### ** Examples
> 
> 
> library(igraph)
Error in library(igraph) : there is no package called ‘igraph’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘optimx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nimble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'iNZightPlots', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'expss', 'hms', 'iNZightTools', 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'forcats', 'dplyr', 'dbplyr', 'ggbeeswarm', 'ggmosaic', 'ggplot2',
  'ggridges', 'ggtext', 'ggthemes', 'kableExtra', 'plotly', 'RSQLite',
  'testthat', 'tibble', 'tidyr', 'viridis', 'waffle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'dplyr', 'GGally', 'ggplot2', 'ggrepel', 'ggtext',
  'iNZightPlots', 'patchwork'

Packages suggested but not available for checking:
  'broom.helpers', 'iNZightTools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'purrr', 'readr', 'srvyr', 'stringr', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'expss', 'haven', 'lubridate', 'readxl', 'RSQLite',
  'styler', 'surveyspec', 'testthat', 'tsibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'ggtext', 'patchwork', 'tidyr',
  'tsibble', 'fable', 'fabletools', 'feasts', 'lubridate', 'stringr',
  'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'reshape2', 'viridis'

Packages suggested but not available for checking:
  'testthat', 'colourpicker', 'bsplus', 'kableExtra', 'igraph',
  'RVCompare'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
checkRd: (-1) IOHproblem.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IOHproblem.Rd:46-48: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'matlib', 'randomcoloR', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'economiccomplexity', 'readxl', 'tidyr', 'usethis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) aiPux.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dls2007.Rd:19: Lost braces
    19 | impact. emph{Journal of Applied Psychology}, 92(5), 1380.
       |             ^
checkRd: (-1) paretoXX.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'eurostat', 'tidyr', 'forcats', 'lubridate', 'kableExtra',
  'tibble', 'readxl', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'roxyglobals'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggalluvial'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’, ‘Rf_StringFalse’, ‘Rf_StringTrue’,
    ‘Rf_isBlankString’, ‘SETLENGTH’, ‘SET_NAMED’

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: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vctrs’

Packages suggested but not available for checking:
  'bignum', 'blob', 'dplyr', 'fuzzyjoin', 'pillar', 'testthat',
  'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘treemap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'testthat', 'lubridate', 'eeptools', 'kableExtra',
  'gtsummary', 'stringr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gdistance’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'dplyr', 'lubridate', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'paletteer', 'ggthemes'

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'geobr', 'patchwork', 'purrr', 'testthat',
  'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'readr'

Packages suggested but not available for checking:
  'purrr', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr', 'mlr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking:
  'lme4', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'caret', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'secr', 'stringr'

Packages suggested but not available for checking: 'FrF2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phangorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'GGally', 'magick', 'testthat', 'tidyr', 'huxtable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'haven', 'hipread', 'purrr', 'readr', 'tibble', 'tidyselect'

Packages suggested but not available for checking:
  'dbplyr', 'ggplot2', 'rmapshaper', 'RSQLite', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggforce', 'ggplot2', 'stringr', 'reshape2'

Packages suggested but not available for checking: 'readxl', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mice’
Running examples in ‘IPWboxplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IPW.ASYM.boxplot
> ### Title: Boxplot adapted to skewness and missing values
> ### Aliases: IPW.ASYM.boxplot
> ### Keywords: quantile boxplot missing inverse probability weighted
> 
> ### ** Examples
> 
> 
> ## A real data example
> 
> 
> library(mice)
Error in library(mice) : there is no package called ‘mice’
Execution halted
Package required but not available: ‘geepack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggforce', 'ggplot2', 'plotly', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'mlr', 'devtools'
Packages suggested but not available for checking: 'DiagrammeR', 'Hmisc'
Package required but not available: ‘GGMncv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘repr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'imager', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'twang', 'ggplot2', 'ggthemes', 'rstanarm', 'rvest',
  'DisImpact', 'forcats', 'tidygeocoder', 'tigris', 'tidycensus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DiagrammeR', 'ggplot2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘example-scripts.Rmd’ using rmarkdown
--- finished re-building ‘example-scripts.Rmd’

--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown

Quitting from lines 126-180 [functGraphViz] (getting-started-with-irg.Rmd)
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
there is no package called 'DiagrammeR'
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Invalid NAMESPACE file, parsing gives:
Error in utils::packageVersion("dplyr"): there is no package called ‘dplyr’

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'repr', 'IRdisplay'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) partial_eigen.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) partial_eigen.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:41-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:47-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'ggpubr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
Packages required but not available:
  'tidyr', 'dplyr', 'purrr', 'tibble', 'ggplot2', 'stringr',
  'ChemoSpec', 'hyperSpec'

Packages suggested but not available for checking:
  'kableExtra', 'fda', 'vctrs', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geepack’

Package suggested but not available for checking: ‘MEMSS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readxl', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'usethis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'dplyr', 'purrr', 'reshape2', 'janitor', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'tibble', 'pillar'
Running examples in ‘irt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_empirical_icc2
> ### Title: Plot Empirical Item Characteristic Curve
> ### Aliases: plot_empirical_icc2
> 
> ### ** Examples
> 
> ip <- generate_ip(model = c("3PL", "GRM"), n = 20)
> true_theta <- rnorm(2000)
> resp <- sim_resp(ip = ip, theta = true_theta)
> 
> # Provide item ID
> plot_empirical_icc2(resp = resp, item = "Item_5")
Error in plot_empirical_icc2(resp = resp, item = "Item_5") : 
  This function requires 'ggplot2' package. Please install it using 'install.packages("ggplot2")'
Execution halted
Packages required but not available: 'DiagrammeR', 'tidyr'

Packages suggested but not available for checking: 'lme4', 'reshape2'

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: 'igraph', 'biclust'
Package suggested but not available for checking: ‘xcms’
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tibble', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) analyseISE.Rd:66: Lost braces; missing escapes or markup?
    66 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) analyseISE.Rd:69: Lost braces; missing escapes or markup?
    69 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
checkRd: (-1) describeISE.Rd:71: Lost braces; missing escapes or markup?
    71 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) describeISE.Rd:74: Lost braces; missing escapes or markup?
    74 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qgraph’

Package suggested but not available for checking: ‘IsingSampler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'gganimate', 'ggplot2', 'plotly', 'purrr', 'simlandr',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'IsingFit', 'IsingSampler', 'transformr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'magick', 'testthat'
Specified C++11: please drop specification unless essential
File ‘isoband/libs/isoband.so’:
  Found non-API call to R: ‘SETLENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'stringr', 'readxl', 'dplyr', 'ggplot2', 'ggrepel', 'qgraph',
  'tidyr', 'purrr', 'reshape2'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Run all unit tests
  > 
  > testthat::test_check("isocalcR")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘isocalcR-vignette.Rmd’ using rmarkdown

Quitting from lines 20-25 [setup] (isocalcR-vignette.Rmd)
Error: processing vignette 'isocalcR-vignette.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘isocalcR-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘isocalcR-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dendextend', 'dplyr', 'ggplot2', 'kableExtra'
Error(s) in re-building vignettes:
  ...
--- re-building ‘isocat.Rmd’ using rmarkdown

Quitting from lines 16-33 [setup] (isocat.Rmd)
Error: processing vignette 'isocat.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘isocat.Rmd’

SUMMARY: processing the following file failed:
  ‘isocat.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |     ^
checkRd: (-1) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |           ^
Package required but not available: ‘bsplus’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'tidyr', 'dplyr', 'ggplot2', 'readr', 'tidyselect', 'purrr'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'forcats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tinysnapshot’
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Package required but not available: ‘spaMM’

Packages suggested but not available for checking:
  'elevatr', 'magick', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++14: please drop specification unless essential
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'latex2exp', 'pillar', 'purrr', 'rstan', 'tibble', 'tidyr',
  'tidyselect'

Packages suggested but not available for checking:
  'bayesplot', 'cowplot', 'ggdist', 'ggplot2', 'ggraph', 'igraph',
  'readxl', 'testthat', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DiagrammeR', 'kableExtra'
Package required but not available: ‘R2jags’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'janitor', 'readr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ibd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readxl', 'dplyr', 'tidyr', 'ggplot2', 'rio'

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: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'plotly', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'keras', 'tensorflow'

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.
checkRd: (-1) secretin.Rd:17: Lost braces
    17 |       {\code{a}: 1st sample};
       |       ^
checkRd: (-1) secretin.Rd:18: Lost braces
    18 |       {\code{b}: 2nd sample}.}
       |       ^
checkRd: (-1) secretin.Rd:20: Lost braces
    20 |       {\code{20+}: 20 minutes or longer since injection};
       |       ^
checkRd: (-1) secretin.Rd:21: Lost braces
    21 |       {\code{pre}: before injection.}}
       |       ^
checkRd: (-1) secretin.Rd:23: Lost braces
    23 |       {\code{20}:  20 minutes since injection};
       |       ^
checkRd: (-1) secretin.Rd:24: Lost braces
    24 |       {\code{30+}: 30 minutes or longer since injection};
       |       ^
checkRd: (-1) secretin.Rd:25: Lost braces
    25 |       {\code{pre}: before injection.  }}
       |       ^
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mixOmics’

Packages suggested but not available for checking: 'nnTensor', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Cyclops’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'network', 'xergm.common', 'reshape2', 'igraph', 'dplyr', 'cowplot',
  'ggplot2', 'GGally', 'intergraph', 'sna', 'tnet', 'networkDynamic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'tidyr', 'purrr', 'colourpicker', 'ggsci'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'NMF', 'pcalg'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 45-47 [unnamed-chunk-3] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'NMF'
--- 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: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'readr', 'janitor', 'ggcorrplot', 'tidyr',
  'broom', 'tibble', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'forecast', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'patchwork', 'stringr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'rsample'

Package suggested but not available for checking: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
Packages required but not available:
  'ggplot2', 'ggfortify', 'haven', 'patchwork', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘AER’

Packages suggested but not available for checking: 'testthat', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ivreg', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘locClass’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gurobi', 'cplexAPI', 'testthat', 'AER', 'ggplot2'
checkRd: (-1) sTsls.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}}
       |                                   ^
checkRd: (-1) sTslsSplines.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage
       |                                               ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Packages suggested but not available for checking:
  'AER', 'effects', 'testthat', 'gt', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Package required but not available: ‘vctrs’

Packages suggested but not available for checking:
  'clock', 'dplyr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'forecast', 'testthat'
Specified C++11: please drop specification unless essential
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'ggthemes', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'gitear', 'kableExtra', 'lubridate', 'shiny.i18n',
  'stringr', 'purrr'

Packages suggested but not available for checking:
  'tibble', 'readr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'rvest', 'stringr', 'readr'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking:
  'bracer', 'stringr', 'xmlconvert'
Packages required but not available: 'qvalue', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'qspray', 'symbolicQspray', 'DescTools', 'mvp', 'ratioOfQsprays'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qvalue', 'ClusterR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'ggplot2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘JacobiEigen.Rmd’ using rmarkdown

Quitting from lines 100-113 [unnamed-chunk-1] (JacobiEigen.Rmd)
Error: processing vignette 'JacobiEigen.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘JacobiEigen.Rmd’

SUMMARY: processing the following file failed:
  ‘JacobiEigen.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'posterior', 'purrr', 'R2jags', 'targets', 'tarchetypes', 'tibble',
  'tidyselect'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'hms', 'lubridate', 'purrr', 'stringr', 'snakecase',
  'tidyselect', 'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'RSQLite', 'testthat', 'tibble', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'keras', 'tensorflow', 'dplyr', 'purrr', 'forcats', 'readr',
  'ggplot2', 'narray', 'lubridate', 'StatRank'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'pillar', 'progress', 'purrr', 'stringr', 'tibble', 'tidyr',
  'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'R2jags', 'ggplot2', 'ggExtra', 'tidyr', 'kableExtra', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  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'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'readr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kableExtra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Lancement_cruncher.Rmd’ using rmarkdown

Quitting from lines 15-19 [setup] (Lancement_cruncher.Rmd)
Error: processing vignette 'Lancement_cruncher.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘Lancement_cruncher.Rmd’

--- re-building ‘Lancement_cruncher_pdf.Rmd’ using rmarkdown

Quitting from lines 28-34 [setup] (Lancement_cruncher_pdf.Rmd)
Error: processing vignette 'Lancement_cruncher_pdf.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘Lancement_cruncher_pdf.Rmd’

--- re-building ‘Using_the_cruncher_with_JDCruncheR.Rmd’ using rmarkdown

Quitting from lines 15-19 [setup] (Using_the_cruncher_with_JDCruncheR.Rmd)
Error: processing vignette 'Using_the_cruncher_with_JDCruncheR.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘Using_the_cruncher_with_JDCruncheR.Rmd’

--- re-building ‘Using_the_cruncher_with_JDCruncheR_pdf.Rmd’ using rmarkdown

Quitting from lines 28-34 [setup] (Using_the_cruncher_with_JDCruncheR_pdf.Rmd)
Error: processing vignette 'Using_the_cruncher_with_JDCruncheR_pdf.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘Using_the_cruncher_with_JDCruncheR_pdf.Rmd’

SUMMARY: processing the following files failed:
  ‘Lancement_cruncher.Rmd’ ‘Lancement_cruncher_pdf.Rmd’
  ‘Using_the_cruncher_with_JDCruncheR.Rmd’
  ‘Using_the_cruncher_with_JDCruncheR_pdf.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘magick’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'ggplot2', 'readr', 'lubridate', 'narray', 'imputeTS',
  'greybox', 'dplyr', 'fastDummies'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'org.Hs.eg.db', 'AnnotationDbi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bde', 'ggplot2', 'rstan'

Packages suggested but not available for checking:
  'BeyondBenford', 'fairness', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'dynlm'
Running examples in ‘JFE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: durbinH
> ### Title: calculate Sortino Ratio of performance over downside risk
> ### Aliases: durbinH
> 
> ### ** Examples
> 
> 
>   data(macrodata)
>   y=ts(macrodata[,"OECD"],start=c(1961,1),freq=12) #OECD business cycle index
> 
>  out1=dynlm::dynlm(y~L(y,1)+season(y)+trend(y))
Error in loadNamespace(x) : there is no package called ‘dynlm’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘randomcoloR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2'
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
File ‘jinjar/libs/jinjar.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘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:
  'broom', 'broom.mixed', 'dplyr', 'eyetrackingR', 'forcats',
  'ggplot2', 'patchwork', 'readr', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'lubridate', 'purrr', 'readr',
  'rvest', 'stringr', 'tibble', 'tidyselect', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘pkgdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'JMbayes2', 'joineRML', 'rstanarm', 'FastJM', 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                          ^
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                                                                               ^
Packages required but not available: 'dplyr', 'caret', 'timeROC'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'car', 'ggplot2', 'vcdExtra', 'GGally', 'BayesFactor', 'afex',
  'ggridges', 'ggrepel', 'dplyr'

Packages suggested but not available for checking:
  'exact2x2', 'testthat', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'jmv', 'haven', 'testthat'
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'lme4', 'tibble'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’

Packages which this enhances but not available for checking:
  'mice', 'remMap', 'mcen'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘mcmcse’

Packages suggested but not available for checking:
  'ggplot2', 'ggpubr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggrepel', 'ggplot2'

Packages suggested but not available for checking:
  'causaldata', 'devtools', 'WeightIt', 'optmatch', 'optweight',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'tibble'

Package suggested but not available for checking: ‘mitml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fds', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'stringr', 'purrr', 'tidytable'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking:
  'badger', 'testthat', 'dplyr', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adv-functionalities.Rmd’ using rmarkdown
--- finished re-building ‘adv-functionalities.Rmd’

--- re-building ‘aux-functions.Rmd’ using rmarkdown
--- finished re-building ‘aux-functions.Rmd’

--- re-building ‘dplyr-joins.Rmd’ using rmarkdown

Quitting from lines 75-96 [example] (dplyr-joins.Rmd)
Error: processing vignette 'dplyr-joins.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘dplyr-joins.Rmd’

--- re-building ‘main-functionalities.Rmd’ using rmarkdown

Quitting from lines 120-132 [unnamed-chunk-2] (main-functionalities.Rmd)
Error: processing vignette 'main-functionalities.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘main-functionalities.Rmd’

--- re-building ‘merge-wrapper.Rmd’ using rmarkdown
--- finished re-building ‘merge-wrapper.Rmd’

--- re-building ‘messages.Rmd’ using rmarkdown
--- finished re-building ‘messages.Rmd’

SUMMARY: processing the following files failed:
  ‘dplyr-joins.Rmd’ ‘main-functionalities.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'lubridate', 'pillar', 'purrr', 'stringr', 'tibble', 'vctrs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'tibble', 'tidyr', 'vctrs', 'pillar',
  'tidygraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'tibble', 'vctrs'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'pillar', 'purrr', 'stringr', 'tibble', 'tidyr', 'vctrs',
  'navigatr', 'stickyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'packer', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'kknn', 'ggplot2', 'factoextra', 'scran'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'ggsci'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'kableExtra', 'dplyr', 'testthat', 'boral', 'Hmsc', 'ggplot2'
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                             ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces; missing escapes or markup?
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                ^
checkRd: (-1) jSDM_binomial_probit_long_format.Rd:45: Lost braces
    45 | \code{species} \tab numeric or character eqn{n_{obs}}{n_obs}-length vector indicating the species observed, \cr 
       |                                                      ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'molaR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggpubr', 'patchwork'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'purrr', 'tibble', 'tidyselect'

Packages suggested but not available for checking:
  'mediation', 'patchwork', 'roxygen2', 'see', 'stringr', 'testthat',
  'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geepack', 'GGally', 'ggplot2', 'ggpubr', 'haven', 'Hmisc', 'jskm',
  'jstable', 'labelled', 'purrr', 'readr', 'readxl', 'see', 'timeROC'

Packages suggested but not available for checking: 'testthat', 'shinytest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'vctrs', 'testthat'
Running examples in ‘jsonlite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rbind_pages
> ### Title: Combine pages into a single data frame
> ### Aliases: rbind_pages
> 
> ### ** Examples
> 
> # Basic example
> x <- data.frame(foo = rnorm(3), bar = c(TRUE, FALSE, TRUE))
> y <- data.frame(foo = rnorm(2), col = c("blue", "red"))
> rbind_pages(list(x, y))
Error: Required package vctrs not found. Please run: install.packages('vctrs')
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #This file runs all unit tests on every R CMD check.
  > #Comment this out to disable.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'geepack', 'lme4', 'labelled', 'tableone', 'dplyr', 'purrr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rvest', 'tibble', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'purrr', 'stringr', 'readr', 'tibble', 'furrr',
  'pryr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggforce', 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘ess’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'broom', 'broom.mixed', 'huxtable', 'kableExtra', 'lme4', 'lmerTest',
  'pbkrtest', 'weights', 'testthat', 'vdiffr'

Packages which this enhances but not available for checking:
  'brms', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readxl', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'rvest', 'stringr'

Packages suggested but not available for checking: 'readxl', 'testthat'

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:
    pre-release juicr (2017 - 2021)
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'nloptr', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DiagrammeR', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BayesFactor', 'ggplot2', 'stringr', 'Superpower'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggthemes', 'ggplot2', 'ggpubr', 'mice', 'rms', 'lme4'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'purrr', 'readr', 'stringr',
  'tibble', 'usethis'

Packages suggested but not available for checking:
  'janitor', 'readxl', 'rvest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking: 'testthat', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tinysnapshot’
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'clustMD', 'ggplot2', 'Hmisc'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'sqldf', 'igraph'

Packages suggested but not available for checking: 'biomaRt', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dendextend', 'purrr', 'stringr'

Packages suggested but not available for checking:
  'dplyr', 'kanjistat.data', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘aRtsy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'dplyr', 'tidyr', 'ggplot2', 'gganimate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MVN', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'forcats', 'dplyr', 'tidyr', 'stringr', 'purrr'

Packages suggested but not available for checking:
  'broom', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘univariateML’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running examples in ‘kdevine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dkde1d
> ### Title: Working with a kde1d object
> ### Aliases: dkde1d pkde1d, qkde1d, rkde1d pkde1d qkde1d
> 
> ### ** Examples
> 
> data(wdbc)  # load data
> fit <- kde1d(wdbc[, 5])  # estimate density
> dkde1d(1000, fit)        # evaluate density estimate
[1] 0.0003689227
> pkde1d(1000, fit)        # evaluate corresponding cdf
[1] 0.8348244
> qkde1d(0.5, fit)         # quantile function

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: eval_qkde1d(sort(obj$x_cc), x, obj$xmin, obj$xmax, obj$bw)
 2: qkde1d(0.5, fit)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'plotly', 'tidyverse', 'geobr'
checkRd: (-1) kdist.Rd:14: Lost braces; missing escapes or markup?
    14 | The {kdist} functions dk, pk, qk and rk, calculates the K-distribution
       |     ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'reshape2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
prepare_Rd: NEWS.Rd:58: Dropping empty section ‘kelvin INITIAL VERSION 1.0-0 (2012-05-30)’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #
  > # The Hadley-verse is an amazing place: unit testing via testthat
  > # See also  http://r-pkgs.had.co.nz/tests.html
  > #
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tensorflow', 'tfruns'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tfdatasets', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tensorflow', 'tfruns'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tfdatasets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'plotly', 'tidyjson', 'dplyr', 'echarts4r', 'magick'

Packages suggested but not available for checking:
  'keras3', 'tfdatasets', 'testthat', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'testthat', 'nloptr'

Packages suggested but not available for checking: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test_parallel.R’ [1s/2s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                          ^
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                                                                                                   ^
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) ipop-class.Rd:28: Lost braces
    28 |   \item{primal}{Object of class \code{ipop}}{Return the primal of the problem}
       |                                             ^
checkRd: (-1) ipop-class.Rd:29: Lost braces
    29 |   \item{dual}{Object of class \code{ipop}}{Return the dual of the problem}
       |                                           ^
checkRd: (-1) ipop-class.Rd:30: Lost braces
    30 |   \item{how}{Object of class \code{ipop}}{Return information on convergence}
       |                                          ^
Package required but not available: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'readxl', 'org.Hs.eg.db'
checkRd: (-1) compute_all_tests.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) subjOCCDIF.Rd:23: Lost braces
    23 | the scale on which to evaluate each subject. \code{stype = "ObsScore"} uses the subject's total score. \code{stype = "Theta"} uses the subject's rank on the \code{thetadist} scale. \code{stype = "ThetaML"} uses the maximum likelihood estimate for the subject on the \code{thetadist} scale. code{stype = "ScoreML"} uses the maximum likelihood estimate for the subject on the overall test score scale.
       |                                                                                                                                                                                                                                                                                                       ^
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'stringr'

Packages suggested but not available for checking: 'shinytest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'purrr', 'stringr', 'tibble', 'tidyr',
  'tidyselect'

Packages suggested but not available for checking: 'readtext', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'sna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mockery', 'testthat'
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) useKeys.Rd:13: Lost braces; missing escapes or markup?
    13 | This function adds the {keys} dependencies to your application
       |                        ^
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'simstandard'

Package suggested but not available for checking: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'testthat'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Note: skipping ‘KFAS.Rnw’ due to unavailable dependencies: 'lme4'
checkRd: (-1) kfda.Rd:26: Lost braces
    26 |  \item{kpca.train}{An object of class "kpca". It has results of \code{kpca} function. (see{\code{\link[kernlab]{kpca}}} (in package \pkg{kernlab}))}
       |                                                                                           ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using knitr

Quitting from lines 26-28 [first-chunk] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
could not find function "qplot"
--- 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: 'ggplot2', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fdapace', 'fda'

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 suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘tibble’
Error in get(f, envir = code_env) : 
  cannot return a promise (PROMSXP) object
Calls: <Anonymous> -> Filter -> unlist -> lapply -> FUN -> get
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'httr2', 'janitor', 'lubridate', 'purrr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'ggraph', 'tinysnapshot'
Running examples in ‘khroma-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_crameri_acton
> ### Title: Fabio Crameri's _acton_ Sequential Color Scheme
> ### Aliases: scale_crameri_acton scale_colour_acton scale_color_acton
> ###   scale_fill_acton scale_edge_colour_acton scale_edge_color_acton
> ###   scale_edge_fill_acton
> 
> ### ** Examples
> 
> data(faithfuld, package = "ggplot2")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘ggplot2’
Calls: data -> find.package
Execution halted
Packages required but not available:
  'stringr', 'purrr', 'rio', 'tibble', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSQLite’

Packages suggested but not available for checking:
  'ggplot2', 'dbplyr', 'tidyr', 'stringr', 'ggthemes', 'ggrepel',
  'dplyr', 'testthat', 'gt', 'purrr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘pryr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Packages required but not available:
  'ggplot2', 'readr', 'ggrepel', 'tibble', 'plotly', 'dplyr',
  'tidyselect', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kinematics.Rcheck/vign_test/kinematics/vignettes/example_files/figure-html/parabolic-plot-1.png
576x480 pixels, 8 bits/pixel, 239 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3427 bytes
Input file size = 4234 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 2852
  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 = 2852

Output IDAT size = 2852 bytes (575 bytes decrease)
Output file size = 2930 bytes (1304 bytes = 30.80% decrease)


Quitting from lines 131-136 [ggplot] (example.Rmd)
Error: processing vignette 'example.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'DNAmixturesLite', 'gRaven', 'gRbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘httr2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) kissmig.Rd:32: Lost braces
    32 | migration in species distribution models (\doi{10.1111/ecog.00930}{Nobis and Normand 2014}).
       |                                                                   ^
checkRd: (-1) kissmig.Rd:86: Lost braces
    86 | \item{\doi{10.1111/ecog.00930}{Nobis MP and Normand S (2014)} KISSMig - a simple model for R to account for
       |                               ^
Packages suggested but not available for checking:
  'dplyr', 'tibble', 'testthat'
Running examples in ‘kitagawa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cross_spectrum
> ### Title: Calculate the cross-spectrum of two timeseries
> ### Aliases: cross_spectrum cross_spectrum.mts cross_spectrum.default
> 
> ### ** Examples
> 
> require(stats)
> require(psd)
Loading required package: psd
Loaded psd (2.1.1) -- Adaptive multitaper spectrum estimation; see ?pspectrum
> 
> n <- 1000
> ramp <- seq_len(n)
> parab <- ramp^2
> 
> set.seed(1255)
> X <- ts(rnorm(n) + ramp/2)
> Y <- ts(rnorm(n) + ramp/10 + parab/100)
> 
> # Calculate the multitaper cross spectrum
> csd <- cross_spectrum(X, Y, k=20)
Error in loadNamespace(x) : there is no package called ‘tibble’
Calls: cross_spectrum ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'tibble', 'lubridate', 'dplyr', 'purrr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ExtDist’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘questionr’

Package which this enhances but not available for checking: ‘clustMixType’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'kableExtra'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package which this enhances but not available for checking: ‘rkward’
checkRd: (-1) klausuR.answ-class.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:18-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:114-116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:117-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:124-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:152-155: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'tibble'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘coca’

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:
  'dplyr', 'GGally', 'ggforce', 'ggplot2', 'ggrepel', 'metR', 'tibble',
  'tidyselect'

Packages suggested but not available for checking: 'testthat', 'RGeostats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘klsh.Rmd’ using rmarkdown

Quitting from lines 163-179 [unnamed-chunk-7] (klsh.Rmd)
Error: processing vignette 'klsh.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘klsh.Rmd’

SUMMARY: processing the following file failed:
  ‘klsh.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'testthat'
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                        ^
checkRd: (-1) plotkmc.Rd:21: Lost braces; missing escapes or markup?
    21 |     list of two functions,flist=list( f1=function( x ) { x } ,f2=function( x ) { x^2 } )  
       |                                                                                ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'factoextra', 'ggplot2', 'caret'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dendextend', 'testthat'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kmer-vignette.Rmd’ using rmarkdown

Quitting from lines 140-160 [unnamed-chunk-5] (kmer-vignette.Rmd)
Error: processing vignette 'kmer-vignette.Rmd' failed with diagnostics:
there is no package called 'dendextend'
--- failed re-building ‘kmer-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘kmer-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'cowplot', 'ggplot2', 'pammtools', 'tidyr'

Packages suggested but not available for checking:
  'broom', 'devtools', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘RefManageR’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'ggplot2', 'igraph', 'reshape2'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'purrr', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example_progress_bars.Rmd’ using rmarkdown

Quitting from lines 131-134 [test_pb_null] (example_progress_bars.Rmd)
Error: processing vignette 'example_progress_bars.Rmd' failed with diagnostics:
there is no package called 'purrr'
--- failed re-building ‘example_progress_bars.Rmd’

--- re-building ‘multiprocessing.Rmd’ using rmarkdown
--- finished re-building ‘multiprocessing.Rmd’

SUMMARY: processing the following file failed:
  ‘example_progress_bars.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘Killed after ’
Packages suggested but not available for checking:
  'magick', 'styler', 'targets', 'tibble'
Running ‘run-all.R’ [15s/26s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testit)
  > test_pkg("knitr")
  
  Error from withRestarts(stop(cond), retry_loadNamespace = function() NULL) 
  Error in loadNamespace(x) : there is no package called 'tibble'
  Calls: test_pkg ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  In addition: Warning messages:
  1: In write_bib(pkgs, tempfile(), tweak = FALSE) :
    package(s) KernSmooth, MASS, boot, class, cluster, foreign, mgcv, nlme, nnet, rpart, spatial, survival not found
  2: In write_bib(pkgs, tweak = TRUE) :
    package(s) KernSmooth, MASS, boot, class, cluster, foreign, mgcv, nlme, nnet, rpart, spatial, survival not found
  Execution halted
Packages required but not available: 'purrr', 'readr', 'stringr'

Packages suggested but not available for checking: 'testthat', 'waldo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘tsibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'caret', 'psycho'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) knockoff.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knockoff.Rd:25-27: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'rgbif', 'car', 'candisc'
checkRd: (-1) MapPolygon.Rd:20: Lost braces
    20 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
checkRd: (-1) SurveyQ.Rd:26: Lost braces
    26 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readxl', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'broom.mixed', 'dplyr', 'ggplot2', 'purrr', 'tidyr', 'lme4',
  'tibble', 'ggrepel', 'pbkrtest'

Packages suggested but not available for checking:
  'devtools', 'forcats', 'mice', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking:
  'testthat', 'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ../inst/tests
  > 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_check("koRpus")
  Error in test_check("koRpus") : could not find function "test_check"
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pcalg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) kpmt.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) compose.Rd:13: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) compose.Rd:14: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) EGIparallel.Rd:60: Lost braces; missing escapes or markup?
    60 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) max_sur_parallel.Rd:29: Lost braces; missing escapes or markup?
    29 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_timse_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion. 
       |                                    ^
checkRd: (-1) max_vorob_parallel.Rd:30: Lost braces; missing escapes or markup?
    30 | Finally, one can control the field {optim.option} in order to decide how to optimize the sampling criterion.
       |                                    ^
checkRd: (-1) print_uncertainty_nd.Rd:72: Lost braces
    72 | Optional argument. When set to code{NULL} (default) the function performs the projections on plans spanned by each pair (i,j) of dimension. Otherwise, the argument is an array of size 2 corresponding to the dimensions spanning the (only) plan on which the projection is performed.
       |                                    ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## load dependencies
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) Predict_kernel_Ridge_MM.Rd:45: Lost braces; missing escapes or markup?
    45 |   and alpha_train is the BLUP of alpha for the model, i.e. alpha_train=Cov(alpha,Y_train)*Var(Y_train)^{-1}*(Y_train - E[Y_train]) }
       |                                                                                                        ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ks_test_stat.Rd:14: Lost braces
    14 | are valid. See /code{LcKS} for accepted functions.}
       |                     ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pryr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
Packages suggested but not available for checking: 'FactoClass', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ##
  > ##  Unit testing file
  > ##
  > ##  Created by Daniel Rodriguez Perez on 7/12/2014.
  > ##
  > ##  Copyright (c) 2014 Daniel Rodriguez Perez.
  > ##
  > ##  This program is free software: you can redistribute it and/or modify
  > ##  it under the terms of the GNU General Public License as published by
  > ##  the Free Software Foundation, either version 3 of the License, or
  > ##  (at your option) any later version.
  > ##
  > ##  This program is distributed in the hope that it will be useful,
  > ##  but WITHOUT ANY WARRANTY; without even the implied warranty of
  > ##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > ##  GNU General Public License for more details.
  > ##
  > ##  You should have received a copy of the GNU General Public License
  > ##  along with this program.  If not, see <http://www.gnu.org/licenses/>
  > ## 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'ggplot2', 'forecast', 'imputeTS', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'kstMatrix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GSE’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rockchalk’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'lme4', 'Hmisc', 'magick'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixtools', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'igraph', 'caret', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) predict.l2boost.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Packages suggested but not available for checking: 'ggplot2', 'latex2exp'
Error(s) in re-building vignettes:
  ...
--- re-building ‘l2e-intro.Rmd’ using rmarkdown

Quitting from lines 214-264 [unnamed-chunk-12] (l2e-intro.Rmd)
Error: processing vignette 'l2e-intro.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘l2e-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘l2e-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'ggraph', 'vctrs'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) reconcile.Rd:26: Lost braces
    26 | refer to as the sQuote{comm} data.frame.  The other data.frame contains all the
       |                       ^
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'haven', 'dplyr', 'vctrs', 'stringr', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'testthat', 'questionr', 'snakecase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'car', 'nycflights13', 'tibble', 'haven', 'dplyr', 'modelr',
  'ggplot2'
Running examples in ‘labelr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_base_data_frame
> ### Title: Convert Augmented Data Frame to Base R Data Frame
> ### Aliases: as_base_data_frame adf
> 
> ### ** Examples
> 
> x1 <- runif(10)
> x2 <- as.character(sample(c(1:20), 10, replace = TRUE))
> x3 <- sample(letters, size = 10, replace = TRUE)
> df <- data.frame(x1, x2, x3)
> dft <- tibble::as_tibble(df)
Error in loadNamespace(x) : there is no package called ‘tibble’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages suggested but not available for checking: 'Hmisc', 'testthat'
Running ‘tests-all.R’ [0s/1s]
Running the tests in ‘tests/tests-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'smooth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'purrr', 'tibble'

Packages suggested but not available for checking: 'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘Rcmdr’
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘FrF2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'janitor', 'sjmisc', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'httptest', 'mockery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'ggtext', 'patchwork', 'lubridate',
  'stringr', 'tidyr', 'forcats'

Packages suggested but not available for checking:
  'bsplus', 'datapasta', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘run_testthattests.R’ [0s/1s]
Running the tests in ‘tests/run_testthattests.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'stringr', 'tidyr', 'tibble', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'purrr', 'tidyr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) laf_open.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{model}{a {data model}, such as one returned by \link{read_dm} or
       |                ^
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'tibble', 'tidyr', 'progress'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'ggplot2', 'reshape2', 'tidyr', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'R2jags', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) lambda.r-package.Rd:71-74: Lost braces
    71 | x \%g\% y \%:=\% {
       |                  ^
Packages required but not available:
  'car', 'purrr', 'ggplot2', 'readr', 'stringr', 'lubridate', 'narray',
  'imputeTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘lme4’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'riskRegression', 'dplyr', 'pec', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GenerateData.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:59-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:67-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DOS.Rd:34: Lost braces; missing escapes or markup?
    34 |         Band-specific sensor $G_{rescale}$ (gain). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
checkRd: (-1) DOS.Rd:37: Lost braces; missing escapes or markup?
    37 |         Band-specific sensor $B_{rescale}$ (bias). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'stringr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'testthat'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Running examples in ‘langevitour-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: knnDenoise
> ### Title: k-nearest neighbor denoising of a set of points
> ### Aliases: knnDenoise
> 
> ### ** Examples
> 
> library(palmerpenguins)
> 
> completePenguins <- na.omit(penguins[,c(1,3,4,5,6)])
Error in na.omit(penguins[, c(1, 3, 4, 5, 6)]) : 
  cannot return a promise (PROMSXP) object
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage.Rmd’ using rmarkdown

Quitting from lines 28-39 [unnamed-chunk-2] (usage.Rmd)
Error: processing vignette 'usage.Rmd' failed with diagnostics:
cannot return a promise (PROMSXP) object
--- failed re-building ‘usage.Rmd’

SUMMARY: processing the following file failed:
  ‘usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'rms', 'Hmisc', 'lme4', 'lmerTest', 'optimx'
Packages required but not available: 'roxygen2', 'styler'

Packages suggested but not available for checking:
  'mockery', 'purrr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'tidyr', 'reshape2', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) LML.Rd:43: Lost braces
    43 |     is specified only with the \code{GD}, code{HME}, or \code{NSIS}
       |                                               ^
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) MISS.Rd:106: Lost braces
   106 |   code{Fit$Imp}. In the presence of numerous missing values, say more
       |       ^
checkRd: (-1) Matrices.Rd:316: Lost braces
   316 |   Gauss-Hermite quadrature rules. A grid of order eqn{K} provides an
       |                                                      ^
checkRd: (-1) PMC.Rd:214: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |       ^
checkRd: (-1) PMC.Rd:214-215: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |           ^
checkRd: (-1) caterpillar.plot.Rd:15: Lost braces
    15 |     code{demonoid.hpc}, \code{iterquad}, \code{laplace}, \code{pmc},
       |         ^
Packages suggested but not available for checking: 'testthat', 'devtools'
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘lares’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'patchwork', 'rvest', 'stringr',
  'tidyr'

Packages suggested but not available for checking:
  'beepr', 'DALEX', 'googlesheets4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘treemap’

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: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'heatmaply', 'ggplot2', 'plotly'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EGAnet', 'googledrive', 'mlr'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'network', 'ergm', 'sna'

Package suggested but not available for checking: ‘heplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'styler', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/r-lib/testthat/issues/86
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'testthat', 'waldo', 'ggplot2', 'purrr', 'tibble', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'pkgdown', 'devtools', 'lme4', 'mixtools',
  'fda', 'funFEM', 'igraph', 'dtwclust', 'mixAK', 'qqplotr', 'simTool',
  'dplyr', 'ggplot2', 'caret', 'tibble'
Running examples in ‘latrend-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lcMethodFlexmix
> ### Title: Method interface to flexmix()
> ### Aliases: lcMethodFlexmix
> 
> ### ** Examples
> 
> data(latrendData)
> if (require("flexmix")) {
+   method <- lcMethodFlexmix(Y ~ Time, id = "Id", time = "Time", nClusters = 3)
+   model <- latrend(method, latrendData)
+ }
Loading required package: flexmix
Loading required package: lattice
---------------------------------------------------------------------------
- Longitudinal clustering using: flexmix
---------------------------------------------------------------------------
Method arguments:
 formula.mb:     ~1
 time:           "Time"
 id:             "Id"
 nClusters:      3
 cluster:        NULL
 model:          NULL
 control:        NULL
 weights:        NULL
 formula:        Y ~ Time
---------------------------------------------------------------------------
Checking and transforming the training data format.
Preparing the training data for fitting...
Fitting the method...
Error in .checkPackageInstalled(name) : 
  The "lme4" package is required. Install the package to use this method.
	Run: install.packages("lme4")
Calls: latrend ... getREterms -> .loadOptionalPackage -> .checkPackageInstalled
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
latrendBoot 4.72   0.39    7.02
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Note: skipping ‘demo.Rmd’ due to unavailable dependencies: 'ggplot2'
Note: skipping ‘implement.Rmd’ due to unavailable dependencies: 'ggplot2'
Note: skipping ‘simulation.Rmd’ due to unavailable dependencies: 'ggplot2'
Packages required but not available:
  'stringr', 'mpoly', 'ggplot2', 'dplyr', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
checkRd: (-1) VignetteExamples.Rd:25: Lost braces; missing escapes or markup?
    25 |  See Section 4 in the {LatticeKrig Vignette} for the use of these data.
       |                       ^
Packages suggested but not available for checking:
  'rempsyc', 'lavaanPlot', 'tidySEM', 'tibble', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'DiagrammeR', 'stringr', 'dplyr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'geepack', 'igraph', 'lavaSearch2', 'lme4', 'optimx', 'targeted',
  'testthat'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > #library("lava")
  > suppressPackageStartupMessages(library("testthat"))
  Error in library("testthat") : there is no package called 'testthat'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking:
  'lme4', 'lmerTest', 'pbkrtest', 'riskRegression', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘revdbayes’

Packages suggested but not available for checking:
  'eva', 'testthat', 'texmex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'vctrs', 'tibble'

Packages suggested but not available for checking:
  'bench', 'dplyr', 'forcats', 'ggplot2', 'ggbeeswarm', 'slider',
  'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'dipsaus'
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘forecast’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
File ‘lazyeval/libs/lazyeval.so’:
  Found non-API call to R: ‘R_PromiseExpr’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tibble', 'dbplyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'readr', 'stringr', 'dplyr', 'tibble', 'lubridate', 'ggplot2',
  'ReinforcementLearning'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'optimx', 'testthat'
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'trekcolors'

Packages suggested but not available for checking:
  'testthat', 'ggrepel', 'leaflet.extras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
Packages required but not available: 'bsplus', 'ggplot2', 'plotly'

Packages suggested but not available for checking: 'xcms', 'MSnbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'ggplot2', 'broom', 'semPlot', 'stringr',
  'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'rvest', 'highcharter', 'tidyr', 'ldatuning',
  'textmineR', 'chinese.misc', 'stringr', 'ggrepel', 'qgraph',
  'factoextra'

Packages suggested but not available for checking: 'beepr', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'batchtools', 'dendextend', 'progress'

Packages suggested but not available for checking: 'testthat', 'tosca'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'reshape2', 'ggplot2'
Packages required but not available:
  'beepr', 'broom', 'chinese.misc', 'dplyr', 'highcharter',
  'ldatuning', 'plotly', 'purrr', 'stringr', 'textmineR', 'tidyr',
  'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'progress', 'viridis'

Packages suggested but not available for checking:
  'pkgdown', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gistr’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'latex2exp', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'caretEnsemble', 'lares', 'ggplot2', 'janitor'

Packages suggested but not available for checking:
  'Cubist', 'tidyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'GUniFrac', 'phangorn'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'keras', 'devtools', 'tensorflow'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'updog', 'VariantAnnotation'
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'patchwork'
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ldsr.Rmd’ using rmarkdown

Quitting from lines 48-52 [unnamed-chunk-1] (ldsr.Rmd)
Error: processing vignette 'ldsr.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘ldsr.Rmd’

SUMMARY: processing the following file failed:
  ‘ldsr.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'systemfit'
Running examples in ‘ldt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estim.sur
> ### Title: Estimate a SUR Model
> ### Aliases: estim.sur
> 
> ### ** Examples
> 
> # Example 1 (simulation, small model):
> set.seed(123)
> sample <- sim.sur(sigma = 2L, coef = 3L, nObs = 100)
> print(sample$coef)
                  Y1         Y2
Intercept -0.5604756 0.07050839
X1        -0.2301775 0.12928774
X2         1.5587083 1.71506499
> print(sample$sigma)
          Y1        Y2
Y1 1.8128237 0.2472081
Y2 0.2472081 0.6703814
> 
> data <- data.frame(sample$y, sample$x)
> 
> #    Use systemfit to estimate:
> exp_names <- paste0(colnames(sample$x), collapse = " + ")
> fmla <- lapply(1:ncol(sample$y), function(i) as.formula(paste0("Y", i, " ~ -1 +", exp_names)))
> fit <- systemfit::systemfit(fmla, data = data, method = "SUR")
Error in loadNamespace(x) : there is no package called ‘systemfit’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'shinytest', 'dplyr', 'rmapshaper'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Connection_to_other_elements.Rmd’ using rmarkdown
--- finished re-building ‘Connection_to_other_elements.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 32-40 [setup] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Introduction.Rmd’

--- re-building ‘Multilevel.Rmd’ using rmarkdown

Quitting from lines 28-36 [setup] (Multilevel.Rmd)
Error: processing vignette 'Multilevel.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Multilevel.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction.Rmd’ ‘Multilevel.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘leaflet.extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

Packages suggested but not available for checking: 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 37-51 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- 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: ‘testthat’
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'purrr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

Packages which this enhances but not available for checking:
  'geojsonio', 'mapedit'

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:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘geojsonio’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘sva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘opencpu’

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: ‘testthat’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readxl', 'haven', 'readODS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'forcats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ChemoSpec', 'roxut', 'latex2exp', 'plotly'
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'roxygen2', 'devtools'
Packages suggested but not available for checking:
  'RSQLite', 'shinytest2', 'testthat'
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'tidyr', 'tibble', 'tidyselect'

Packages suggested but not available for checking: 'rio', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmmTMB', 'lme4'

Package suggested but not available for checking: ‘Rcompadre’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'greybox', 'smooth', 'nloptr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'testthat', 'purrr', 'stringr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'readr', 'stringr', 'httr2', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'brms', 'ggplot2', 'usethis', 'ggpubr', 'purrr', 'stringr', 'readxl',
  'dplyr', 'rio', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'sccore'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'bipartite', 'devtools', 'graphsim', 'multinet', 'network',
  'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'furrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'stringr', 'dplyr', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tidyselect’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'usethis', 'roxygen2'

Packages suggested but not available for checking: 'packer', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'haven', 'readODS', 'arrow'
Packages required but not available: 'ggplot2', 'tidyr', 'stringr'

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: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'devtools', 'dplyr', 'kableExtra', 'ggplot2'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tibble', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'pkgdown', 'styler', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘syuzhet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

Packages suggested but not available for checking:
  'corpustools', 'dplyr', 'RSQLite', 'testthat', 'tidytext',
  'kableExtra', 'striprtf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘HMDHFDplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'shinyFiles', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DESeq2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘lfc_vignette.Rmd’ using rmarkdown

Quitting from lines 35-47 [unnamed-chunk-1] (lfc_vignette.Rmd)
Error: processing vignette 'lfc_vignette.Rmd' failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘lfc_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘lfc_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘igraph’
File ‘lfe/libs/lfe.so’:
  Found non-API call to R: ‘SET_NAMED’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘biascorrection.Rnw’ using knitr
--- finished re-building ‘biascorrection.Rnw’

--- re-building ‘identification.Rnw’ using knitr
--- finished re-building ‘identification.Rnw’

--- re-building ‘lfehow.Rnw’ using knitr
--- finished re-building ‘lfehow.Rnw’

--- re-building ‘speed.Rnw’ using knitr

Quitting from lines 144-156 [unnamed-chunk-9] (speed.Rnw)
Error: processing vignette 'speed.Rnw' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘speed.Rnw’

SUMMARY: processing the following file failed:
  ‘speed.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'readr', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'VIM', 'dplyr', 'vsn', 'reshape2', 'ggplot2', 'Hmisc', 'tidyr',
  'plotly', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) flowunit.Rd:30: Lost braces; missing escapes or markup?
    30 | Usually flow units are of dimension $L^3 T^{-1}$. Currently a length $l$ can be on of \code{c("metre", "cm", "centimetre" "litre")}, whereas time $T$ can be one in \code{c("days", "hours", "mins", "secs")}, possibly abbreviated. The numerator of the fraction (everything before the literal \code{"/"}) is interpreted as the length (superscripts like \code{"^3"} are discarded), the denominator as time. E.g. valid units would be \code{"cm^3/s"}, \code{"m^3/day"} or \code{"litre/sec"}.
       |                                            ^
checkRd: (-1) seasindex.Rd:30: Lost braces
    30 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing
       |                 ^
checkRd: (-1) seasindex.Rd:34: Lost braces
    34 | Mitteilungen, Inst. f{\"u}r Wasserbau u. Ingenieurhydrologie,
       |                      ^
checkRd: (-1) seasratio.Rd:31: Lost braces
    31 | Laaha, G. and Bl{\"o}schl, G. (2006), Seasonality indices for regionalizing low flows. Hydrol. Process., 20
       |                 ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'monobin'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'bayesplot', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'localgauss', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Packages suggested but not available for checking:
  'gmailr', 'RMariaDB', 'RPostgres', 'RSQLite', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘geepack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'devtools'
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dij.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{i}{A positive integer, which stands for the i^{th} row of \code{X}.}
       |                                                     ^
checkRd: (-1) dij.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{j}{A positive integer, which stands for the j^{th} row of \code{X}. Both \code{i} and \code{j} should be in [1,nrow(X)] and they should not be equal to each other.}
       |                                                     ^
checkRd: (-1) exchange.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{A positive integer, which stands for the j^{th} column (or row) of \code{X}, and it should be within [1,ncol(X)] (or [1,nrow(X)]).}
       |                                                     ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_for_LHD.Rmd’ using rmarkdown

Quitting from lines 26-28 [unnamed-chunk-2] (Vignette_for_LHD.Rmd)
Error: processing vignette 'Vignette_for_LHD.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘Vignette_for_LHD.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette_for_LHD.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

Packages suggested but not available for checking: 'assertr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘igraph’
checkRd: (-1) isingdata.Rd:14: Lost braces; missing escapes or markup?
    14 |     \item{X}{a 5000-by-100 matrix, each entry is in {-1,1}.}
       |                                                     ^
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
Running examples in ‘Libra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ising
> ### Title: Linearized Bregman solver for composite conditionally likelihood
> ###   of Ising model with lasso penalty.
> ### Aliases: ising
> ### Keywords: regression
> 
> ### ** Examples
> 
> 
> library('Libra')
> library('igraph')
Error in library("igraph") : there is no package called ‘igraph’
Execution halted
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'readr', 'readxl', 'haven', 'dplyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'fmtr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) libstable4u-package.Rd:16: Lost braces; missing escapes or markup?
    16 | \item Fast and accurate evaluation of the quantile function (CDF^{-1}).
       |                                                                  ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'imager', 'car', 'reldist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mapedit', 'progress', 'testthat'
File ‘lidR/libs/lidR.so’:
  Found non-API calls to R: ‘R_curErrorBuf’, ‘SETLENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘markovchain’

Packages suggested but not available for checking:
  'demography', 'forecast', 'testthat', 'StMoMo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'tibble', 'tidyverse', 'vctrs'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘communicate.Rmd’ using rmarkdown
--- finished re-building ‘communicate.Rmd’

--- re-building ‘manage.Rmd’ using rmarkdown

Quitting from lines 34-38 [unnamed-chunk-3] (manage.Rmd)
Error: processing vignette 'manage.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘manage.Rmd’

--- re-building ‘stages.Rmd’ using rmarkdown
--- finished re-building ‘stages.Rmd’

SUMMARY: processing the following file failed:
  ‘manage.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Hmisc', 'optimx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘LifeInsureR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'MortalityTables', 'lubridate', 'dplyr', 'stringr', 'kableExtra',
  'tidyr'

Packages suggested but not available for checking: 'tibble', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'lubridate', 'modelr', 'stringr', 'tidyr',
  'fitbitScraper', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'maptiles', 'readr', 'stringr', 'tidyterra'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) lx_list_lights.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pavo', 'testthat'
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘likelihoodAsy.Rnw’ using knitr

Quitting from lines 730-735 [Random intercept example] (likelihoodAsy.Rnw)
Error: processing vignette 'likelihoodAsy.Rnw' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘likelihoodAsy.Rnw’

SUMMARY: processing the following file failed:
  ‘likelihoodAsy.Rnw’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) likelihood_calculation.Rd:24: Lost braces
    24 | For eqn{i = 1\dots N} independent observations in a vector \var{X}, with individual observations \eqn{x_i}{xi}, and a set of parameter values \eqn{\theta}:
       |        ^
checkRd: (-1) simulated_annealing_algorithm.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:27: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'caret', 'dplyr', 'ggplot2', 'M3C', 'pathview', 'RCy3',
  'stringr', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'progress', 'tidyr'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'beepr', 'ggplot2', 'keras', 'dplyr', 'readr'

Package suggested but not available for checking: ‘textclean’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'mlr', 'magick', 'keras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tourr', 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'testthat'
Running examples in ‘limonaid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: processLimeSurveyDropouts
> ### Title: Process LimeSurvey dropouts
> ### Aliases: processLimeSurveyDropouts
> 
> ### ** Examples
> 
> limonaid::processLimeSurveyDropouts(c(1,2,1,1,2,3,2,2,3,2,1));
Error in limonaid::processLimeSurveyDropouts(c(1, 2, 1, 1, 2, 3, 2, 2,  : 
  To process the LimeSurvey dropouts, you need to have both the {ggplot2} and {ggrepel} packages installed. You can install them with:

  install.packages(c('ggplot2', 'ggrepel'));
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘DESeq2’

Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'annotate', 'ggplot2', 'org.Mm.eg.db', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library('testthat')
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 22-30 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'annotate'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'viridis', 'tidyr', 'readr', 'forecast'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'styler'
Packages suggested but not available for checking:
  'roxygen2', 'devtools', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kableExtra’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'pkgdown', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'sna', 'network'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 19-23 [setup] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'igraph', 'intergraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'downlit', 'httr2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘AER’
Packages suggested but not available for checking:
  'mockery', 'patrick', 'testthat', 'tibble'
Running examples in ‘lintr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: expect_lint
> ### Title: Lint expectation
> ### Aliases: expect_lint
> 
> ### ** Examples
> 
> # no expected lint
> expect_lint("a", NULL, trailing_blank_lines_linter())
Error in expect_lint("a", NULL, trailing_blank_lines_linter()) : 
  'expect_lint' is designed to work within the 'testthat' testing framework, but 'testthat' is not installed.
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'reshape2', 'shadowtext', 'stringr', 'tableone',
  'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'broom', 'car', 'ggiraph', 'rcompanion', 'tidyr',
  'cowplot', 'dplyr', 'ggplot2', 'ggplotify', 'ggrepel', 'reshape2',
  'stringr', 'tidyselect', 'ggforce', 'ggsci'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cowplot', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'tibble', 'purrr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'dplyr'
Running examples in ‘listcompr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gen.logical.and
> ### Title: Generate Logical Conditions with List Comprehension
> ### Aliases: gen.logical.and gen.logical.or
> 
> ### ** Examples
> 
> # Returns a_1 == 1 & a_2 == 2 & a_3 == 3
> gen.logical.and(a_i == i, i = 1:3)
a_1 == 1L & (a_2 == 2L & a_3 == 3L)
> 
> # A data frame of tuples (x_1, x_2, x_3, x_4) summing up to 10 with x_i <= x_(i+1)
> gen.data.frame(c(x_1, ..., x_4), x_ = 1:10, x_1 + ... + x_4 == 10, 
+                gen.logical.and(x_i <= x_(i+1), i = 1:3))
  x_1 x_2 x_3 x_4
1   2   2   3   3
2   1   3   3   3
3   2   2   2   4
4   1   2   3   4
5   1   1   4   4
6   1   2   2   5
7   1   1   3   5
8   1   1   2   6
9   1   1   1   7
> 
> # Get all permutations of 1:4
> gen.data.frame(c(a_1, ..., a_4), a_ = 1:4, 
+                gen.logical.and(a_i != a_j, i = 1:4, j = (i+1):4))
   a_1 a_2 a_3 a_4
1    4   3   2   1
2    3   4   2   1
3    4   2   3   1
4    2   4   3   1
5    3   2   4   1
6    2   3   4   1
7    4   3   1   2
8    3   4   1   2
9    4   1   3   2
10   1   4   3   2
11   3   1   4   2
12   1   3   4   2
13   4   2   1   3
14   2   4   1   3
15   4   1   2   3
16   1   4   2   3
17   2   1   4   3
18   1   2   4   3
19   3   2   1   4
20   2   3   1   4
21   3   1   2   4
22   1   3   2   4
23   2   1   3   4
24   1   2   3   4
>                
> # Get again the permutations of 1:4, using filter from dplyr 
> df <- gen.data.frame(c(a_1, ..., a_4), a_ = 1:4)
> dplyr::filter(df, !!gen.logical.and(a_i != a_j, i = 1:3, j = (i+1):4))
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 132-135 [unnamed-chunk-12] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- 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: ‘tibble’

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'purrr'

Package which this enhances but not available for checking: ‘workflowr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arm’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyselect’

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘RSQLite’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tibble'
File ‘literanger/libs/literanger.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘revdbayes’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘genio’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'devtools'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'readr', 'stringr', 'dplyr', 'tidyselect', 'tidyr', 'ggplot2',
  'purrr'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) vcov.liu.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear Liu regression model for scalar or vector biasing parameter \code{d}{d} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{d}{d}.}
       |                                                                                                                             ^
Packages required but not available:
  'mlr', 'dplyr', 'breakDown', 'forestmodel', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'DALEX'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘skimr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'caret', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'reghelper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggrepel', 'ggforce', 'fmdu', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'patchwork'

Packages suggested but not available for checking: 'ggformula', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dynutils’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

Packages suggested but not available for checking:
  'MEMSS', 'testthat', 'ggplot2', 'mlmRev', 'optimx', 'gamm4',
  'pbkrtest', 'car', 'rr2', 'semEff', 'tibble', 'merDeriv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'scdhlm', 'mlmRev', 'lme4', 'merDeriv'
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggdist', 'HLMdiag', 'purrr', 'forcats', 'tidyr',
  'tibble'

Packages suggested but not available for checking:
  'lme4', 'testthat', 'mlmRev'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'ggplot2'

Package suggested but not available for checking: ‘pbkrtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘lme4’
Running examples in ‘lmfor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plants
> ### Title: Sapling counts from sample plots of sapling stands in Finland.
> ### Aliases: plants
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(plants)
> library(lme4)
Error in library(lme4) : there is no package called ‘lme4’
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'patchwork', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lmls.Rmd’ using rmarkdown

Quitting from lines 23-45 [setup] (lmls.Rmd)
Error: processing vignette 'lmls.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘lmls.Rmd’

SUMMARY: processing the following file failed:
  ‘lmls.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'loo', 'rstan'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'asht', 'ggh4x', 'ggpubr', 'lme4', 'lmerTest', 'mice', 'optimx',
  'reshape2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'kableExtra'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LMN.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LMN.Rcheck/vign_test/LMN/vignettes/LMN_files/figure-html/toy_sim_calc-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14092 bytes
Input file size = 14182 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10778
  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 = 10778

Output IDAT size = 10778 bytes (3314 bytes decrease)
Output file size = 10856 bytes (3326 bytes = 23.45% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LMN.Rcheck/vign_test/LMN/vignettes/LMN_files/figure-html/toysim-1.png
624x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24295 bytes
Input file size = 24397 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 19307
  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 = 19307

Output IDAT size = 19307 bytes (4988 bytes decrease)
Output file size = 19385 bytes (5012 bytes = 20.54% decrease)


Quitting from lines 271-293 [unnamed-chunk-4] (LMN.Rmd)
Error: processing vignette 'LMN.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘LMN.Rmd’

SUMMARY: processing the following file failed:
  ‘LMN.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘SPEI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'genefilter', 'progress'

Packages suggested but not available for checking: 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) vcov.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear ridge regression model for scalar or vector biasing parameter \code{K}{K} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{K}{K}.}
       |                                                                                                                               ^
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'car', 'dynlm', 'AER'
Packages suggested but not available for checking: 'testthat', 'twang'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'WeightIt', 'PSweight', 'ivreg', 'mlogit', 'testthat'
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mcmcse’
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'echarts4r', 'readxl', 'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Package required but not available: ‘OpenStreetMap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'pillar', 'pkgdown', 'testthat'
Specified C++11: please drop specification unless essential
File ‘lobstr/libs/lobstr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘viridis’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Specified C++11: please drop specification unless essential
Note: skipping ‘LocalControl-jss-2020.Rnw’ due to unavailable dependencies:
  'ggplot2'
Found the following HTML validation problems:
UPSLTDdist.html:54:1 (UPSLTDdist.Rd:17): Warning: trimming empty <dt>
plot.LocalControlCR.html:63:1 (plot.LocalControlCR.Rd:29): Warning: trimming empty <dt>
plot.LocalControlCS.html:59:1 (plot.LocalControlCS.Rd:24): Warning: trimming empty <dt>
Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'dplyr', 'readr', 'tidyr', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LocalCop-vignette.Rmd’ using rmarkdown

Quitting from lines 22-30 [setup] (LocalCop-vignette.Rmd)
Error: processing vignette 'LocalCop-vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘LocalCop-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘LocalCop-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sampleSelection’

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DALEX', 'ggplot2', 'ingredients'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'httr2', 'readr', 'stringr', 'tibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) FootballBrain.Rd:15: Lost braces; missing escapes or markup?
    15 |     { } \tab {or \code{FBConcuss}=football player with concussion history} \cr
       |     ^
checkRd: (-1) HappyPlanetIndex.Rd:14: Lost braces; missing escapes or markup?
    14 |     { } \tab {\code{5}=South Asia, \code{6}=East Asia, \code{7}=former Communist countries}\cr
       |     ^
checkRd: (-1) RockandRoll2012.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) RockandRoll2015.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) StudentSurvey.Rd:12: Lost braces; missing escapes or markup?
    12 |     \item{\code{Sex}}{code {F}=female or \code{M}=male}
       |                            ^
checkRd: (-1) SynchronizedMovement.Rd:16: Lost braces; missing escapes or markup?
    16 |     { } \tab {for High/Low Synchronization + High/Low Exertion}\cr
       |     ^
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘bigsnpr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ensembldb', 'gggrid', 'ggplot2', 'ggrepel',
  'plotly'

Packages suggested but not available for checking:
  'AnnotationHub', 'EnsDb.Hsapiens.v75'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'metR', 'viridis'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘run-all.R’ [0s/1s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'caretEnsemble', 'dplyr', 'ggplot2', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'slackr', 'testthat', 'devtools', 'roxygen2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘run_tests.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/run_tests.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lubridate', 'readxl'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cookies', 'emayili', 'stringr'

Package which this enhances but not available for checking: ‘RSQLite’

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: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'fda', 'fda.usc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘logitnorm.Rmd’ using knitr

Quitting from lines 7-30 [setup] (logitnorm.Rmd)
Error: processing vignette 'logitnorm.Rmd' failed with diagnostics:
could not find function "exit"
--- failed re-building ‘logitnorm.Rmd’

SUMMARY: processing the following file failed:
  ‘logitnorm.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'nloptr', 'tibble'

Packages suggested but not available for checking:
  'apollo', 'broom', 'dplyr', 'fastDummies', 'ggplot2', 'ggrepel',
  'gmnl', 'gtsummary', 'kableExtra', 'mixl', 'mlogit', 'testthat',
  'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
checkRd: (-1) logdensity.Rd:33: Lost braces; missing escapes or markup?
    33 | The function \code{logdensity} computes kernel density estimates (KDE) of strictly positive distributions by performing the KDE in the log domain and then transforming the result back again. The syntax and function structure is largely borrowed from the function \code{density} in package {stats}.
       |                                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) logdensity_fft.Rd:33: Lost braces; missing escapes or markup?
    33 | The function \code{logdensity_fft} computes kernel density estimates (KDE) of strictly positive distributions by performing the KDE via fast fourier transform utilizing the \code{fft} function. The syntax and function structure is largely borrowed from the function \code{density} in package {stats}.
       |                                                                                                                                                                                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'purrr', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # workaround for error LC_CTYPE failed, using "C" but does not work
  > #https://github.com/r-lib/testthat/issues/86
  > #Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lognorm.Rmd’ using rmarkdown

Quitting from lines 17-40 [setup] (lognorm.Rmd)
Error: processing vignette 'lognorm.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘lognorm.Rmd’

--- re-building ‘lognormalDiff.Rmd’ using rmarkdown

Quitting from lines 16-39 [setup] (lognormalDiff.Rmd)
Error: processing vignette 'lognormalDiff.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘lognormalDiff.Rmd’

--- re-building ‘lognormalSum.Rmd’ using rmarkdown

Quitting from lines 16-39 [setup] (lognormalSum.Rmd)
Error: processing vignette 'lognormalSum.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘lognormalSum.Rmd’

SUMMARY: processing the following files failed:
  ‘lognorm.Rmd’ ‘lognormalDiff.Rmd’ ‘lognormalSum.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'tidylog', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'Tplyr', 'haven', 'readr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'network', 'ggplot2', 'reshape2', 'intergraph'

Packages suggested but not available for checking:
  'testthat', 'ergm', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'latex2exp', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'plotly'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

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:
  'lme4', 'reshape2', 'glmmTMB', 'bestNormalize', 'ggplot2', 'stringr',
  'tibble', 'dplyr', 'car', 'rstatix', 'tidyr', 'patchwork'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available: 'AICcmodavg', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyr', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘latex2exp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'fdapace', 'dplyr', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘StatMatch’

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'ggplot2', 'ggalluvial', 'FactoMineR',
  'factoextra', 'lme4', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'ggpubr', 'purrr', 'reshape2',
  'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'dplyr', 'tidyr', 'fdapace', 'lme4', 'tibble', 'purrr',
  'readr', 'refund', 'fda', 'fda.usc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'TDAstats', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) SAheart.Rd:96: Lost braces
    96 |   J.E. Rossouw, J.P.D. Plessis, A.J.S. Benad\'{e}, P.C.J. Jordaan, 
       |                                               ^
checkRd: (-1) SAheart.Rd:97: Lost braces
    97 |   J.P. Kotz\'{e}, P.L. Jooste, and J.J. Ferreira (1983)
       |              ^
Packages required but not available: 'ggplot2', 'ggmulti', 'patchwork'

Packages suggested but not available for checking:
  'GGally', 'tidyr', 'dplyr', 'tibble', 'testthat', 'nycflights13'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) l_binCut.Rd:30: Lost braces
    30 | when 'code{labels = FALSE}, the default \code{active} is  \code{-1}; and when \code{labels} is a vector of length equal
       |           ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'loon.ggplot', 'colourpicker'

Packages suggested but not available for checking:
  'dplyr', 'ggmulti', 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tourr', 'loon.ggplot', 'tibble'

Packages suggested but not available for checking: 'tidyverse', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘posterior’

Packages suggested but not available for checking:
  'bayesplot', 'brms', 'ggplot2', 'rstan', 'rstanarm', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Packages suggested but not available for checking:
  'testthat', 'rstan', 'bridgesampling'
Error(s) in re-building vignettes:
  ...
--- re-building ‘LoRaD-gtrig-vignette.Rmd’ using rmarkdown
--- finished re-building ‘LoRaD-gtrig-vignette.Rmd’

--- re-building ‘bridge-sampling.Rmd’ using rmarkdown

Quitting from lines 34-37 [unnamed-chunk-2] (bridge-sampling.Rmd)
Error: processing vignette 'bridge-sampling.Rmd' failed with diagnostics:
there is no package called 'rstan'
--- failed re-building ‘bridge-sampling.Rmd’

--- re-building ‘lorad-k80-vignette.Rmd’ using rmarkdown
--- finished re-building ‘lorad-k80-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘bridge-sampling.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dineq’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) qut.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{q}{A number between \code{0} and \code{1}. The quantile of the distribution of $lambda_{QUT}$ to take.}
       |                                                                                              ^
checkRd: (-1) qut.Rd:25: Lost braces; missing escapes or markup?
    25 | the value of $lambda_{QUT}$ to use in LoRI.
       |                      ^
Package required but not available: ‘geomorph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat) # nolint
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lotri-motivation.Rmd’ using rmarkdown

Quitting from lines 36-42 [unnamed-chunk-2] (lotri-motivation.Rmd)
Error: processing vignette 'lotri-motivation.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘lotri-motivation.Rmd’

SUMMARY: processing the following file failed:
  ‘lotri-motivation.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'plotly'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘RSQLite’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSQLite’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘locits’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘lphom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: error_lphom
> ### Title: Global error of a lphom estimated table
> ### Aliases: error_lphom
> 
> ### ** Examples
> 
> mt.lphom <- lphom(France2017P[, 1:8], France2017P[, 9:12], 
+                   new_and_exit_voters = "raw", verbose = FALSE)
> set.seed(253443)
> example <- error_lphom(mt.lphom, upper.alfa = 0.10, show.plot = FALSE, num.d = 5, B = 8)
Error: Package ggplot2 needed for this function to work. Please install it.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'readxl', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'LPGraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'reshape2', 'ggplot2', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'LPGraph', 'LPBkg', 'nloptr', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘lpSolveAPI/libs/lpSolveAPI.so’:
  Found non-API call to R: ‘SETLENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'ggplot2', 'devtools'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LPWC.Rmd’ using rmarkdown

Quitting from lines 146-174 [unnamed-chunk-4] (LPWC.Rmd)
Error: processing vignette 'LPWC.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘LPWC.Rmd’

SUMMARY: processing the following file failed:
  ‘LPWC.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) SKD.Rd:76: Lost braces; missing escapes or markup?
    76 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
checkRd: (-1) best.lqr.Rd:66: Lost braces; missing escapes or markup?
    66 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
checkRd: (-1) cens.lqr.Rd:70: Lost braces; missing escapes or markup?
    70 | \author{Christian E. Galarza <\email{chedgala@espol.edu.ec}>, {Marcelo Bourguignon} <\email{m.p.bourguignon@gmail.com}> and
       |                                                               ^
checkRd: (-1) logbestlqr.Rd:86: Lost braces; missing escapes or markup?
    86 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
checkRd: (-1) loglqr.Rd:98: Lost braces; missing escapes or markup?
    98 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
checkRd: (-1) lqr-package.Rd:22: Lost braces; missing escapes or markup?
    22 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and 
       |                                                              ^
checkRd: (-1) lqr.Rd:83: Lost braces; missing escapes or markup?
    83 | \author{Christian E. Galarza <\email{cgalarza88@gmail.com}>, {Luis Benites} <\email{lsanchez@ime.usp.br}> and
       |                                                              ^
Package required but not available: ‘DoseFinding’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Cued_Recall.Rmd’ using rmarkdown
--- finished re-building ‘Cued_Recall.Rmd’

--- re-building ‘Free_Recall.Rmd’ using rmarkdown

Quitting from lines 24-34 [unnamed-chunk-1] (Free_Recall.Rmd)
Error: processing vignette 'Free_Recall.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Free_Recall.Rmd’

--- re-building ‘Multi_Recall.Rmd’ using rmarkdown

Quitting from lines 24-35 [unnamed-chunk-1] (Multi_Recall.Rmd)
Error: processing vignette 'Multi_Recall.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Multi_Recall.Rmd’

--- re-building ‘Sentence_Recall.Rmd’ using rmarkdown
--- finished re-building ‘Sentence_Recall.Rmd’

SUMMARY: processing the following files failed:
  ‘Free_Recall.Rmd’ ‘Multi_Recall.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr'
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘direct_approximation_vs_schoenfeld.Rmd’ using rmarkdown
--- finished re-building ‘direct_approximation_vs_schoenfeld.Rmd’

--- re-building ‘fixed_follow-up.Rmd’ using rmarkdown
--- finished re-building ‘fixed_follow-up.Rmd’

--- re-building ‘group_sequential_multiplicity.Rmd’ using rmarkdown

Quitting from lines 232-274 [simulated number of events and p-values] (group_sequential_multiplicity.Rmd)
Error: processing vignette 'group_sequential_multiplicity.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘group_sequential_multiplicity.Rmd’

--- re-building ‘group_sequential_simulation.Rmd’ using rmarkdown
--- finished re-building ‘group_sequential_simulation.Rmd’

--- re-building ‘maxcombo.Rmd’ using rmarkdown
--- finished re-building ‘maxcombo.Rmd’

--- re-building ‘non-proportional_hazards.Rmd’ using rmarkdown
--- finished re-building ‘non-proportional_hazards.Rmd’

--- re-building ‘stratified.Rmd’ using rmarkdown
--- finished re-building ‘stratified.Rmd’

SUMMARY: processing the following file failed:
  ‘group_sequential_multiplicity.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'EnvStats', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lme4', 'Hmisc'

Packages suggested but not available for checking:
  'BIFIEsurvey', 'miceadds', 'mice', 'difR', 'kerdiest', 'car', 'mitml'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

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: ‘TSdist’

Package suggested but not available for checking: ‘LSDsensitivity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'LSDinterface', 'LSDsensitivity'
Packages required but not available: 'LSDinterface', 'sensitivity', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'plotly'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'dplyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘LSMRealOptions.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LSMRealOptions.Rcheck/vign_test/LSMRealOptions/vignettes/LSMRealOptions_files/figure-html/unnamed-chunk-9-1.png
672x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29462 bytes
Input file size = 29576 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 23917
  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 = 23917

Output IDAT size = 23917 bytes (5545 bytes decrease)
Output file size = 23995 bytes (5581 bytes = 18.87% decrease)


Quitting from lines 266-281 [unnamed-chunk-10] (LSMRealOptions.Rmd)
Error: processing vignette 'LSMRealOptions.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘LSMRealOptions.Rmd’

SUMMARY: processing the following file failed:
  ‘LSMRealOptions.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'broom'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lspline.Rmd’ using rmarkdown

Quitting from lines 69-75 [show_data] (lspline.Rmd)
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘lspline.Rmd’

SUMMARY: processing the following file failed:
  ‘lspline.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'ggplot2', 'broom', 'tibble'

Packages suggested but not available for checking:
  'igraph', 'testthat', 'moderndive', 'babynames'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'patchwork'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'reshape2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'readr', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GDINA', 'ggplot2', 'ggpubr', 'ggsignif'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'janitor', 'usethis', 'metajam', 'tidyverse', 'broom', 'ggmap',
  'lubridate', 'patchwork', 'tsibble', 'feasts', 'gt'
Packages required but not available: 'dplyr', 'ggplot2', 'magick', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'readxl', 'stringr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'tibble', 'tidyselect', 'igraph',
  'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'arm'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) k.Rd:27: Lost braces
    27 |  code{\link{ACSPlan-class}}, 
       |      ^
Package suggested but not available for checking: ‘randomForestSRC’
'LazyData' is specified without a 'data' directory
checkRd: (-1) DLSimulate.Rd:38: Lost braces
    38 | code{\link{arima.sim}} 
       |     ^
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘testthat’
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'vctrs'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lubridate.Rcheck/00install.out’ for details.
Package required but not available: ‘rpostgis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'broom', 'dplyr', 'lme4', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lucid_examples.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lucid.Rcheck/vign_test/lucid/vignettes/lucid_examples_files/figure-html/dotplot-1.png
576x384 pixels, 8 bits/pixel, 256 colors in palette
Input IDAT size = 12906 bytes
Input file size = 13776 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11859
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 11621
  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 = 11621

Output IDAT size = 11621 bytes (1285 bytes decrease)
Output file size = 12479 bytes (1297 bytes = 9.41% decrease)


Quitting from lines 172-175 [broom1] (lucid_examples.Rmd)
Error: processing vignette 'lucid_examples.Rmd' failed with diagnostics:
could not find function "%>%"
--- failed re-building ‘lucid_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘lucid_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'networkD3', 'progress'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'caret', 'Hmisc'
Running examples in ‘lulcc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: allow
> ### Title: Implement decision rules for land use change
> ### Aliases: allow
> 
> ### ** Examples
> 
> 
> ## Plum Island Ecosystems
> 
> ## load observed land use data
> obs <- ObsLulcRasterStack(x=pie,
+                    pattern="lu",
+                    categories=c(1,2,3),
+                    labels=c("forest","built","other"),
+                    t=c(0,6,14))
> 
> ## get land use values
> x <- getValues(obs[[1]])
> x <- x[!is.na(x)]
> 
> ## create vector of arbitrary land use history values
> hist <- sample(1:10, length(x), replace=TRUE)
> 
> ## calculate demand and get change direction for first timestep
> dmd <- approxExtrapDemand(obs=obs, tout=0:14)
Warning in total(x = obs) :
  missing argument 'categories': getting categories from 'x'
Error in loadNamespace(x) : there is no package called ‘Hmisc’
Calls: approxExtrapDemand ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘readxl’

Packages suggested but not available for checking:
  'plotly', 'testthat', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'progress', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'ggplot2', 'dplyr', 'tfevents', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) LVGP_fit.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_fit.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LVGP_predict.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) math_example.Rd:21: Lost braces
    21 | Data are sampled from the modified math function based on the first example in the paper listed in code{references}.
       |                                                                                                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) StEM_pcirt.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{response}{N by J matrix containing {0,1,...,M-1} responses, where N is the number of respondents and J is the number of items.}
       |                                          ^
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'purrr', 'rsample', 'tibble',
  'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'devtools', 'forcats', 'lme4', 'lmerTest', 'testthat', 'usethis',
  'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'dplyr', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tibble'

Package suggested but not available for checking: ‘depth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘test-all.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘azimuth.R’ [1s/1s]
  Comparing ‘azimuth.Rout’ to ‘azimuth.Rout.save’ ... OK
  Running ‘dist.R’ [1s/3s]
  Comparing ‘dist.Rout’ to ‘dist.Rout.save’ ... OK
  Running ‘geod.R’ [1s/2s]
  Comparing ‘geod.Rout’ to ‘geod.Rout.save’ ... OK
  Running ‘perimeter.R’ [1s/2s]
  Comparing ‘perimeter.Rout’ to ‘perimeter.Rout.save’ ... OK
  Running ‘testthat.R’ [0s/1s]
  Running ‘twkb.R’ [1s/1s]
  Comparing ‘twkb.Rout’ to ‘twkb.Rout.save’ ... OK
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'gWQS', 'gamm4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/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)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'caret'

Packages suggested but not available for checking: 'moveHMM', 'DiagrammeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mpoly', 'stringr', 'usethis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'InterSIM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GenomicFeatures’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readxl’

Packages suggested but not available for checking: 'testthat', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mixtools’
checkRd: (-1) mable.dr.Rd:23: Lost braces
    23 | \item{x, y}{original two sample raw data, code{x}:"Control", \code{y}: "Case".}
       |                                               ^
checkRd: (-1) mable.dr.group.Rd:26: Lost braces
    26 | specified by \code{t}. code{n0}:"Control", \code{n1}: "Case".}
       |                            ^
checkRd: (-1) mable.reg.Rd:50: Lost braces
    50 | Wrapping all code{mable} fit of regression models in one function.
       |                  ^
checkRd: (-1) maple.dr.Rd:23: Lost braces
    23 | \item{x, y}{original two sample raw data, code{x}:"Control", \code{y}: "Case".}
       |                                               ^
checkRd: (-1) maple.dr.group.Rd:27: Lost braces
    27 | specified by \code{t}. code{n0}:"Control", \code{n1}: "Case".}
       |                            ^
Package suggested but not available for checking: ‘roxygen2’
Packages required but not available: 'lme4', 'optimx', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dials', 'ggplot2', 'progress', 'recipes', 'rsample', 'tibble'

Packages suggested but not available for checking:
  'adabag', 'C50', 'censored', 'Hmisc', 'kableExtra', 'kknn',
  'ParBayesianOptimization', 'parsnip', 'randomForestSRC', 'rms',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'etl', 'dplyr', 'lubridate', 'phenocamr', 'readr', 'rvest', 'stringr'

Packages suggested but not available for checking:
  'ggplot2', 'dbplyr', 'RSQLite', 'broom', 'purrr', 'clifro',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'strex'

Package suggested but not available for checking: ‘rnaturalearthhires’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'igraph', 'tidyr', 'reshape2', 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mediation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'textmineR', 'tidytext', 'tidyr', 'dplyr', 'hwordcloud', 'stringr',
  'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'textmineR', 'tidytext', 'tidyr', 'dplyr', 'hwordcloud', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mada-data.Rd:45: Lost braces
    45 | Kriston, L., H{\"o}elzel, L., Weiser, A., Berner, M., & Haerter, M. (2008).\dQuote{ Meta-analysis: Are 3
       |               ^
Package suggested but not available for checking: ‘ggplot2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘maddison_project_database.Rmd’ using rmarkdown

Quitting from lines 27-32 [unnamed-chunk-1] (maddison_project_database.Rmd)
Error: processing vignette 'maddison_project_database.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘maddison_project_database.Rmd’

SUMMARY: processing the following file failed:
  ‘maddison_project_database.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'lubridate'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # /usr/bin/r
  > #
  > # Copyright 2015-2015 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > #
  > # This file is part of madness.
  > #
  > # madness is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU Lesser General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # madness is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU Lesser General Public License for more details.
  > #
  > # You should have received a copy of the GNU Lesser General Public License
  > # along with madness.  If not, see <http://www.gnu.org/licenses/>.
  > #
  > # Created: 2015.11.28
  > # Copyright: Steven E. Pav, 2015
  > # Author: Steven E. Pav <shabbychef@gmail.com>
  > # Comments: Steven E. Pav
  > 
  > # because Hadley says it should be like this.
  > # see https://github.com/hadley/devtools/wiki/Testing
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introducing_madness.Rnw’ using knitr

Quitting from lines 1148-1202 [preamble] (introducing_madness.Rnw)
Error: processing vignette 'introducing_madness.Rnw' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘introducing_madness.Rnw’

SUMMARY: processing the following file failed:
  ‘introducing_madness.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘MAd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotcon
> ### Title: Meta Regression Scatterplot
> ### Aliases: plotcon
> ### Keywords: aplot
> 
> ### ** Examples
> 
> # SAMPLE DATA
> MA2 <-read.table(textConnection("
+ id       es1       var1 n.1 n.2 mod1 mod2
+ 1   1 0.5695938 0.04906967  26  30    a   20
+ 2   2 0.4123667 0.04362541  28  34    b   30
+ 3   3 0.4084333 0.04458363  34  28    a   25
+ 4   4 0.5014756 0.04186354  37  29    b   35
+ 5   5 0.5540745 0.04339382  31  32    b   40
+ 6   1 0.5695938 0.04906967  26  30    a   20
+ 7   2 0.4123667 0.04362541  28  34    b   30
+ 8   3 0.4084333 0.04458363  34  28    a   25
+ 9   4 0.5014756 0.04186354  37  29    b   35
+ 10  5 0.5540745 0.04339382  31  32    b   40"))
> 
> 
> # EXAMPLE
> plotcon(es1, var1, mod2, data=MA2, method= "fixed", modname="NULL",title="NULL")
Error: Package "ggplot2" must be installed to use this function.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'stringr', 'ggplot2', 'tidytext', 'lubridate', 'janitor',
  'forcats', 'haven', 'readr', 'tidyr', 'fabR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lpjmlkit', 'quitte', 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'SeqVarTools', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘imager’
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘magick’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'gapminder', 'IRdisplay'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/magick.Rcheck/00install.out’ for details.
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'purrr', 'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'gganimate', 'plotly', 'testthat', 'transformr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.