Packages suggested but not available for checking: 'dittoSeq', '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:
  'tidyverse', 'ggplot2', 'janitor', 'overlapping', 'purrr', 'tibble',
  'dplyr', 'tidyselect'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘magrittr/libs/magrittr.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘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
Packages required but not available: 'tidyr', 'ggplot2'

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

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: 'gmailr', 'googledrive', 'purrr'

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'tidyr', 'tmap'

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

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

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: ‘tibble’

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: ‘dplyr’

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

Quitting from lines 143-146 [unnamed-chunk-14] (makeit.Rmd)
Error: processing vignette 'makeit.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘makeit.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) makeProject.Rd:34: Lost braces
    34 | email{noahsilverman@ucla.edu}
       |      ^
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
Packages required but not available:
  'dplyr', 'tidygraph', 'igraph', 'tibble'

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:
  'ggplot2', 'dplyr', 'tidyr', 'tidyterra', 'ows4R', 'lubridate',
  'stringr'

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

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:
  '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’
Running ‘testthat.R’ [0s/1s]
Running 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: '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
Error(s) in re-building vignettes:
  ...
--- re-building ‘mallet.Rmd’ using rmarkdown

Quitting from lines 63-66 [unnamed-chunk-6] (mallet.Rmd)
Error: processing vignette 'mallet.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘mallet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'readr'
Running ‘testthat.R’ [0s/1s]
Running 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’

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: ‘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: 'imager', '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.
checkRd: (-1) MangroveTree.Rd:37: Lost braces
    37 |       An object of class \\code{\link[Mangrove]{MangrovePed}}
       |                                ^
Packages required but not available: 'plotly', '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: 'reshape2', '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:
  'purrr', 'readr', 'dplyr', 'tidyselect', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'haven', 'readxl', '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
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: 'plotly', 'testthat'
checkRd: (-1) manipulateWidget.Rd:113-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:121-123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manipulateWidget.Rd:124-127: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running 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: ‘DescTools’
Packages suggested but not available for checking:
  'tidyr', 'ggplot2', 'testthat'
checkRd: (-1) EEGwide.Rd:30-33: Lost braces
    30 |   if(requireNamespace("ggplot2")){ 
       |                                  ^
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:
  'biomaRt', 'caret', 'dplyr', 'ggplot2', 'keras', 'purrr', 'reshape2',
  'scutr', 'stringr', 'tibble', 'tidyr', 'tidyselect', 'ggcorrplot'

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', 'messydates', 'purrr', 'stringr', 'usethis', 'ggplot2',
  'tidyr'

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

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

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

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

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

Packages suggested but not available for checking:
  'concaveman', 'gganimate', 'ggforce', 'graphlayouts', 'migraph',
  'patchwork', 'readxl', 'roxygen2', 'testthat', 'furrr'

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 suggested but not available for checking: 'igraph', 'testthat'
checkRd: (-1) shortestpath.Rd:19: Lost braces; missing escapes or markup?
    19 | \eqn{0} means there exists no path for node \eqn{i} and {j}.
       |                                                         ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'smooth'

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

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

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

Packages suggested but not available for checking:
  'ggspatial', 'tigris', 'tidycensus', 'tmap', 'mapboxer', '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: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'ggplot2'
Package suggested but not available for checking: ‘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
Packages required but not available: 'dplyr', 'leaflet.extras', 'leafpm'

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

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
Packages required but not available: 'dplyr', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'progress'
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Packages required but not available:
  'dplyr', 'furrr', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'landscapemetrics', 'rvest', 'testthat'

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

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:
  'tmap', 'ggplot2', 'dplyr', 'geojsonio', 'stringr'

Package suggested but not available for checking: ‘DiagrammeR’

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:
  'ggpubr', 'ggsci', 'dplyr', 'reshape2', 'ggplot2', 'smacof',
  'dendextend', 'vcfR', 'plotly'

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

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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ggplot2', 'dplyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mapsapi.Rcheck/vign_test/mapsapi/vignettes/intro_files/figure-html/unnamed-chunk-26-1.png
1344x960 pixels, 8 bits/pixel, 243 colors in palette
Input IDAT size = 204277 bytes
Input file size = 205384 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 192944
  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 = 192944

Output IDAT size = 192944 bytes (11333 bytes decrease)
Output file size = 193763 bytes (11621 bytes = 5.66% decrease)


Quitting from lines 261-267 [unnamed-chunk-27] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'magick', 'purrr', 'slippymath', 'tibble'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mkMapFinland
> ### Title: Make map of Finland
> ### Aliases: mkMapFinland
> 
> ### ** Examples
> 
> hv.alueet<-mkMapFinland(url="https://tinyurl.com/hvalueet2022")
trying URL 'https://tinyurl.com/hvalueet2022'
downloaded 1.1 MB

> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> ggplot(hv.alueet) +geom_sf()+ggtitle("Wellbeing services counties")
Error in ggplot(hv.alueet) : could not find function "ggplot"
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'slippymath', 'testthat', 'tidyterra'
Running examples in ‘mapSpain-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: esp_get_can_box
> ### Title: Get 'sf' lines and polygons for insetting the Canary Islands
> ### Aliases: esp_get_can_box esp_get_can_provinces
> 
> ### ** Examples
> 
> 
> Provs <- esp_get_prov()
> Box <- esp_get_can_box()
> Line <- esp_get_can_provinces()
> 
> # Plot
> 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 required but not available: ‘tibble’

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:
  > # 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: 'Hmisc', 'reshape2'

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

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:
  > # 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: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', '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: ‘lubridate’
checkRd: (-1) locate_shift.Rd:29: Lost braces
    29 | \code{\link{quickfit}}, code{\link{locator}}
       |                             ^
checkRd: (-1) marcher-package.Rd:14: Lost braces; missing escapes or markup?
    14 | 1. \code{\link{estimate_shift}} {Estimate a range shift process.}
       |                                 ^
checkRd: (-1) marcher-package.Rd:16: Lost braces; missing escapes or markup?
    16 | 2. \code{\link{simulate_shift}} {Simulate a range shift process.}
       |                                 ^
checkRd: (-1) marcher-package.Rd:18: Lost braces; missing escapes or markup?
    18 | 3. \code{\link{plot.shiftfit}} {Visualize a range shift process.}
       |                                ^
checkRd: (-1) marcher-package.Rd:20: Lost braces; missing escapes or markup?
    20 | 4. \code{\link{test_rangeshift}} {Test whether a range shift occurred.}
       |                                  ^
checkRd: (-1) marcher-package.Rd:22: Lost braces; missing escapes or markup?
    22 | 5. \code{\link{test_return}} {Test whether a migration was a return migration.}
       |                              ^
checkRd: (-1) marcher-package.Rd:24: Lost braces; missing escapes or markup?
    24 | 6. \code{\link{test_stopover}} {Test whether a stopover occurred during a migration.}
       |                                ^
checkRd: (-1) quickfit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickfit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) test_rangeshift.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available:
  'readr', 'dplyr', 'usethis', 'devtools', 'lubridate', 'rvest',
  'scholar', 'purrr', 'stringr', 'tidytext', 'tidyr', 'tidyverse',
  'treemapify', 'tibble', 'widyr', 'igraph'

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 suggested but not available for checking:
  'AER', 'afex', 'bench', 'blme', 'brms', 'brmsmargins', 'broom',
  'car', 'causaldata', 'clarify', 'cjoint', 'DALEXtra',
  'distributional', 'dfidx', 'dplyr', 'equivalence', 'flexsurv',
  'fmeffects', 'geepack', 'ggdist', 'ggokabeito', 'ggplot2', 'ggrepel',
  'glmmTMB', 'haven', 'ivreg', 'kableExtra', 'lme4', 'lmerTest',
  'logistf', 'mice', 'miceadds', 'mlogit', 'mlr3verse', 'optmatch',
  'parsnip', 'patchwork', 'pkgdown', 'posterior', 'purrr', 'REndo',
  'rms', 'robustlmm', 'rsample', 'rstanarm', 'sampleSelection',
  'tibble', 'tidymodels', 'tidyr', 'tidyverse', 'tinysnapshot',
  'workflows', 'testthat'
Packages required but not available:
  'purrr', 'tibble', 'furniture', 'stringr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:28: Lost braces; missing escapes or markup?
    28 | ( if(is.ts(DATA)) { DATA <- as.matrix(data.frame(DATA)) } and a message
       |                   ^
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) markdownInput.Rd:17: Lost braces
    17 | \item{inputId}{The code{input} slot that will be used to access the value.}
       |                        ^
checkRd: (-1) markdownInput.Rd:35: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:36: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) markdownInput.Rd:81-82: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:84-86: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) markdownInput.Rd:89-90: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:64-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:67-69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) moduleMarkdownInput.Rd:72-73: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'optimx', 'kableExtra'

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:
  'ggplot2', 'dplyr', 'reshape2', 'CausalImpact', 'tidyr'

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

Package suggested but not available for checking: ‘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', '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: ‘httptest’

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'testthat'
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright 2014-2020 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of MarkowitzR.
  > #
  > # MarkowitzR 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.
  > #
  > # MarkowitzR 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 MarkowitzR.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2014.05.19
  > # Copyright: Steven E. Pav, 2014-2020
  > # 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 suggested but not available for checking:
  'bench', 'bib2df', 'dplyr', 'haven', 'testthat', 'tibble', 'waldo'
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:
  'RSQLite', 'gdistance', 'reshape2', 'ggplot2'

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

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:
  'devtools', 'roxygen2', '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', 'viridis', 'patchwork'
checkRd: (-1) marqLevAlg-package.Rd:14: Lost braces; missing escapes or markup?
    14 | (GH^{-1}G).
       |     ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘mla.Rmd’ using rmarkdown

Quitting from lines 127-132 [unnamed-chunk-1] (mla.Rmd)
Error: processing vignette 'mla.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘mla.Rmd’

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

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

Packages suggested but not available for checking:
  'ggplot2', 'gt', 'patchwork', '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’
Packages suggested but not available for checking:
  'forecast', 'ggplot2', 'Hmisc', 'marssTMB'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'AnnotationDbi', 'clusterProfiler', 'factoextra', 'FactoMineR',
  'ggnewscale', 'ggrepel', 'kableExtra', 'MAST', 'org.Hs.eg.db',
  'org.Mm.eg.db', 'reshape2', 'stringr', 'textclean', 'wiggleplotr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'forestinventory', 'sae', 'testthat'
Packages required but not available: 'dplyr', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'flashier', 'ebnm'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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'

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

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:
  'patchwork', 'dplyr', 'ggplot2'
checkRd: (-1) hr_levels.Rd:9-12: Lost braces
     9 | kernelBiweight <- function(x, mean = 0, sd = 1) {
       |                                                 ^
checkRd: (-1) hr_levels.Rd:33-36: Lost braces
    33 | kernelCosine <- function(x, mean = 0, sd = 1) {
       |                                               ^
checkRd: (-1) hr_levels.Rd:41-44: Lost braces
    41 | kernelEpanechnikov <- function(x, mean = 0, sd = 1) {
       |                                                     ^
checkRd: (-1) hr_levels.Rd:58-61: Lost braces
    58 | kernelOptCosine <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:65-68: Lost braces
    65 | kernelRectangular <- function(x, mean = 0, sd = 1) {
       |                                                    ^
checkRd: (-1) hr_levels.Rd:72-75: Lost braces
    72 | kernelSquaredCosine <- function(x, mean = 0, sd = 1) {
       |                                                      ^
checkRd: (-1) hr_levels.Rd:79-82: Lost braces
    79 | kernelTriangular <- function(x, mean = 0, sd = 1) {
       |                                                   ^
checkRd: (-1) hr_levels.Rd:86-89: Lost braces
    86 | kernelTricube <- function(x, mean = 0, sd = 1) {
       |                                                ^
checkRd: (-1) hr_levels.Rd:93-96: Lost braces
    93 | kernelTriweight <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:100-103: Lost braces
   100 | kernelUniform <- function(x, mean = 0, sd = 1) {
       |                                                ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘rationale.Rmd’ using rmarkdown

Quitting from lines 19-32 [presetup] (rationale.Rmd)
Error: processing vignette 'rationale.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘rationale.Rmd’

SUMMARY: processing the following file failed:
  ‘rationale.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: 'msigdbr', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) CF2004.Rd:8: Lost braces; missing escapes or markup?
     8 |   \item{X2}{an optional second variable with same length as \code{X}, should the equation be multiple (see Details) {in mm}}
       |                                                                                                                     ^
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'ggspatial', 'lubridate', 'readxl',
  'tidyr', 'tibble'

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: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'readr', '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: ‘gurobi’
checkRd: (-1) Rand.index.Rd:22: Lost braces; missing escapes or markup?
    22 | The two vectors \code{x} and \code{y} must have equal length. Given a set \eqn{S} and two partitions \eqn{X} and \eqn{Y} of \eqn{S}, the Rand index is the proportion of pairs of elements in \eqn{S} (out of all pairs) that are either concordant in both \eqn{X} and \eqn{Y} (i.e., they belong to the same member of \eqn{X} and to the same member of \eqn{Y}) or discordant (i.e., not concordant) in both \eqn{X} and {Y}.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
checkRd: (-1) predict.matchFeat.Rd:21: Lost braces
    21 | The function \code{predict.matchFeat} finds the best matching for new feature vectors relative to an existing set of cluster/class centers. If code{object} results from a call to \code{\link{match.gaussmix}}, the same function is used for prediction (with fixed mean vectors and covariance matrices). In other cases, the function \code{\link{match.template}} is used for prediction. 
       |                                                                                                                                                    ^
Package suggested but not available for checking: ‘ggplot2’
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++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:
  'optmatch', 'cobalt', 'gurobi', 'testthat'
Package required but not available: ‘Hmisc’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Match.Rd:90: Lost braces; missing escapes or markup?
    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
Packages required but not available: 'mice', 'WeightIt'

Package suggested but not available for checking: ‘cobalt’

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: 'stringr', 'imager'

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', 'magick'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
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', 'tidyr', 'tidyselect', 'plotly', 'forecast', 'lubridate'

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: '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: ‘DescTools’

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: ‘progress’

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: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Matrix_eQTL_main.Rd:31: Lost braces; missing escapes or markup?
    31 |     {genepos} in the call of \code{Matrix_eQTL_main} function.
       |     ^
checkRd: (-1) Matrix_eQTL_main.Rd:35: Lost braces; missing escapes or markup?
    35 |     the data frames \code{snpspos} and {genepos}.
       |                                        ^
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Running ‘spelling.R’ [1s/1s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
  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
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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:
  'dplyr', 'pillar', 'purrr', 'stringr', 'tibble', 'tidyr',
  'tidyselect', 'vctrs'

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

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', 'reshape2'
Packages suggested but not available for checking:
  'car', 'cosinor', 'cosinor2'
Packages required but not available: 'dplyr', 'purrr', 'RCLabels', 'tibble'

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

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

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

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

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

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

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

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

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: ‘tibble’
Running examples in ‘maxLik-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidy.maxLik
> ### Title: tidy and glance methods for maxLik objects
> ### Aliases: tidy.maxLik glance.maxLik
> 
> ### ** Examples
> 
> ## Example with a single parameter
> t <- rexp(100, 2)
> loglik <- function(theta) log(theta) - theta*t
> a <- maxLik(loglik, start=2)
> tidy(a)
Error in require_tibble_package() : 
  The `tibble` package must be installed to use tidy() or glance() methods
Calls: tidy -> tidy.maxLik -> require_tibble_package
Execution halted
Package required but not available: ‘igraph’

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

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

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', 'lubridate', 'MazamaCoreUtils', 'MazamaSpatialUtils',
  'readr', 'stringr', 'tidygeocoder'

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

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:
  'MazamaSpatialUtils', 'dplyr', 'MazamaCoreUtils', 'tmap'

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', 'MazamaCoreUtils', 'rmapshaper', 'stringr'

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', 'lubridate', 'MazamaCoreUtils', 'stringr'

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’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright 2017-2017 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of mazealls.
  > #
  > # mazealls 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.
  > #
  > # mazealls 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 mazealls.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2017-10-03
  > # Copyright: Steven E. Pav, 2017-2017
  > # 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
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:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'emojifont', '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', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘check-formula-integral.R’ [2s/3s]
  Running ‘check-formula-variance.R’ [2s/3s]
  Running ‘test-1inf-GB1.R’ [2s/3s]
  Running ‘test-1inf-beta.R’ [2s/3s]
  Running ‘test-1inf-mean.R’ [2s/3s]
  Running ‘test-1inf-shftrncPareto.R’ [2s/3s]
  Running ‘test-1inf-unif.R’ [2s/3s]
  Running ‘test-GB1.R’ [2s/3s]
  Running ‘test-asiacom.R’ [3s/3s]
  Running ‘test-beaonre.R’ [3s/4s]
  Running ‘test-beta.R’ [2s/3s]
  Running ‘test-eecf.R’ [2s/3s]
  Running ‘test-fit-MBBEFDgb.R’ [4s/6s]
  Running ‘test-fit-gbeta.R’ [3s/4s]
  Running ‘test-fit-mbbefd.R’ [4s/5s]
  Running ‘test-fit-oibeta.R’ [3s/5s]
  Running ‘test-fit-oigbeta.R’ [4s/5s]
  Running ‘test-fit-oistpareto.R’ [2s/4s]
  Running ‘test-fit-oiunif.R’ [2s/4s]
  Running ‘test-lossalae.R’ [3s/4s]
  Running ‘test-mbbefd-1stparam.R’ [2s/3s]
  Running ‘test-mbbefd-2ndparam.R’ [2s/3s]
  Running ‘test-rng-mbbefd.R’ [2s/3s]
  Running ‘test-shftrncPareto.R’ [3s/4s]
  Running ‘test-smokedfish.R’ [2s/3s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'PKNCA', 'furrr', '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: ‘network’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sem’

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 suggested but not available for checking: ‘spsurvey’
checkRd: (-1) findDescendingTrans.Rd:29: Lost braces
    29 |    Foster, S.D., Hosack, G.R., J. Monk, Lawrence, E., Barrett, N.S., Williams, A. and Przeslawski, P. (2020) Spatially-Balanced Designs for Transect-Based Surveys. Methods in Ecology and Evolution. emph{11}: 95--105
       |                                                                                                                                                                                                           ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘MBHdesign.rnw’ using knitr

Quitting from lines 213-232 [NNestimate] (MBHdesign.rnw)
Error: processing vignette 'MBHdesign.rnw' failed with diagnostics:
there is no package called 'spsurvey'
--- failed re-building ‘MBHdesign.rnw’

SUMMARY: processing the following file failed:
  ‘MBHdesign.rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'stringr', 'ggplot2', 'caret', 'keras', 'dplyr', 'readr', 'reshape2',
  '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', 'devtools', 'roxygen2'
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', 'R2jags', 'igraph', 'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'R2jags', 'reshape2'

Packages suggested but not available for checking:
  'overlapping', 'ggplot2', 'ggdist', 'igraph', 'Hmisc', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'kangar00'
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) SIGMAS.Rd:17: Lost braces; missing escapes or markup?
    17 | Sigmahat =  (Y^{T} Y)/n;
       |                ^
checkRd: (-1) SIGMAS.Rd:18: Lost braces; missing escapes or markup?
    18 | Sigmahat_fit = (Y^{T}  P_fx  Y)/n;
       |                   ^
checkRd: (-1) matpower.Rd:17: Lost braces; missing escapes or markup?
    17 | The function computes M^{power} for a symmetric matrix M. }
       |                         ^
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', 'cowplot', 'tibble', 'dplyr', 'forcats', 'tidyr', 'purrr'

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

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.
Packages required but not available: 'ggplot2', 'ggpubr'

Package suggested but not available for checking: ‘testthat’

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

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', 'ggrepel', 'plotly'

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:
  'tidyverse', 'PracTools', 'testthat'
Packages required but not available: 'ggplot2', 'reshape2'

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

Package suggested but not available for checking: ‘testthat’

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

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

Quitting from lines 45-50 [leap] (mcgf.Rmd)
Error: processing vignette 'mcgf.Rmd' failed with diagnostics:
there is no package called 'lubridate'
--- failed re-building ‘mcgf.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘roxygen2’
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCbound.precalc1.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Packages required but not available: 'tibble', 'dplyr', 'readr', 'stringr'

Packages suggested but not available for checking:
  'tidyr', 'purrr', '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: 'mcmcr', 'nlist', 'purrr'

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:
  'bayesplot', '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 ‘diagnostic-pkgs.Rmd’ using rmarkdown

Quitting from lines 85-86 [unnamed-chunk-8] (diagnostic-pkgs.Rmd)
Error: processing vignette 'diagnostic-pkgs.Rmd' failed with diagnostics:
there is no package called 'bayesplot'
--- failed re-building ‘diagnostic-pkgs.Rmd’

--- re-building ‘faq.Rmd’ using rmarkdown
Loading required package: coda
--- finished re-building ‘faq.Rmd’

SUMMARY: processing the following file failed:
  ‘diagnostic-pkgs.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.
'LazyData' is specified without a 'data' directory
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 required but not available: ‘ggplot2’

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ecr', 'grapherator', 'ggplot2', 'qgraph', 'viridis', '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:
  'R2jags', 'tidyverse', 'tidybayes', 'dplyr', 'ggplot2', 'readxl',
  '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', 'forcats', 'ggplot2', 'ggthemes', 'googlesheets4', 'magick',
  'odbc'

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: 'forecast', '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: 'DoseFinding', 'dplyr'

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

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', 'devtools', 'DoseFinding'
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'loo', 'bayesplot', 'tidybayes', 'dplyr', 'tidyr', 'tidyselect',
  'tibble', 'stringr', 'ggplot2', 'patchwork'

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

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:
  'DescTools', 'dplyr', 'ggplot2', 'purrr', 'tibble', 'tidyr', 'VCA'

Packages suggested but not available for checking:
  'testthat', 'usethis', '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: ‘mixtools’

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:
  'dplyr', 'ggplot2', 'ggthemes', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Packages required but not available: 'dplyr', 'ggplot2', 'hms', 'lubridate'

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

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

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

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

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’
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: ‘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: 'progress', 'readr', 'stringr'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: linkage
> ### Title: Extended Agglomerative Hierarchical Clustering
> ### Aliases: linkage descval descplot
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## Plot and summary of unweighted arithmetic linkage (UPGMA) dendrogram
> lnk1 <- linkage(UScitiesD)
> plot(lnk1)
> summary(lnk1)
Call:
linkage(prox = UScitiesD,
        type.prox = "distance",
        digits = 0,
        method = "arithmetic",
        weighted = FALSE,
        group = "variable")

Number of objects: 10 

Binary dendrogram: TRUE

Descriptive measures:
      cor       sdr        ac        cc        tb 
0.8101937 0.6998814 0.7059747 0.3055556 0.9316262 
> 
> ## Linkage of similarity data (non-negative correlations)
> sim <- as.dist(cor(EuStockMarkets))
> lnk2 <- linkage(sim, type.prox = "similarity")
> plot(lnk2)
> 
> ## Use function as.dendrogram to plot with package dendextend
> d <- dist(scale(mtcars))  # distances of standardized data
> lnk <- linkage(d, digits = 1, method = "complete")
> lnk.dend <- as.dendrogram(lnk)
> plot(dendextend::set(lnk.dend, "branches_k_color", k = 4),
+      nodePar = list(cex = 0.4, lab.cex = 0.5))
Error in loadNamespace(x) : there is no package called ‘dendextend’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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 suggested but not available for checking: 'testthat', 'tibble'
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: 'testthat', 'psqn'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'leaflet.extras', 'ggplot2', 'dplyr', 'readxl', 'plotly'

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: ‘miceadds’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mdp_example_forest.Rd:36: Lost braces; missing escapes or markup?
    36 | Let {1, ... S} be the states of the forest. the Sth state being the oldest.
       |     ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘smacof’

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

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:
  'babynames', 'dbplyr', 'dplyr', 'ggplot2', 'kableExtra', 'RMariaDB',
  'skimr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'Lahman', 'etl', 'macleish', 'mosaic', 'lubridate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', '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:
  'dcm2', 'dplyr', 'loo', 'posterior', 'rstan', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'cmdstanr', '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
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: ‘dplR’

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

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

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

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

Packages suggested but not available for checking: 'rgexf', 'file2meco'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bhm.mcmc.Rd:37: Lost braces; missing escapes or markup?
    37 |   where \eqn{N_{ij}} denotes the number of times that the error profile \eqn{i} is cited on a report from hospital {j} and \eqn{y_{ij}} is the corresponding number of times that profile \eqn{i} in hospital \eqn{j} was reported with harm.
       |                                                                                                                    ^
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘ggplot2’

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

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: 'arm', 'mice'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'lmerTest', 'pbkrtest'

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', '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: ‘mediation’

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', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', '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 ‘cost-report-analysis.Rmd’ using rmarkdown

Quitting from lines 61-67 [unnamed-chunk-1] (cost-report-analysis.Rmd)
Error: processing vignette 'cost-report-analysis.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘cost-report-analysis.Rmd’

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

SUMMARY: processing the following file failed:
  ‘cost-report-analysis.Rmd’

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

Quitting from lines 23-41 [example3] (MedLEA.Rmd)
Error: processing vignette 'MedLEA.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘MedLEA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) MED.Rd:25: Lost braces
    25 | The vector of treatment assignments of length \eqn{n}. Must be coded as \eqn{\{0,1} {{0,1}}.
       |                                                                                     ^
Packages required but not available: 'HDMT', 'qvalue'

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

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

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

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

Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db'

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

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:
  'car', 'dplyr', 'ggplot2', 'ggridges', '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
Error(s) in re-building vignettes:
  ...
--- re-building ‘model.Rmd’ using rmarkdown
--- finished re-building ‘model.Rmd’

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

Quitting from lines 39-51 [unnamed-chunk-3] (performance.Rmd)
Error: processing vignette 'performance.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘performance.Rmd’

--- re-building ‘article.Rnw’ using knitr

Quitting from lines 863-869 [data] (article.Rnw)
Error: processing vignette 'article.Rnw' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘article.Rnw’

SUMMARY: processing the following files failed:
  ‘performance.Rmd’ ‘article.Rnw’

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

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

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

Packages suggested but not available for checking:
  'readxl', 'haven', 'readODS', 'magick'

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:
  'cowplot', 'ggimage', 'shadowtext'

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

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: ‘gdistance’

Package suggested but not available for checking: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'AER', 'car', 'lme4', 'tibble', 'haven'
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:
  'testthat', 'devtools', 'roxygen2'
'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: 'distill', 'usethis'

Packages suggested but not available for checking: 'pkgdown', '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
Packages required but not available:
  'ggplot2', 'cowplot', 'viridis', 'stringr', 'HH', 'tidyr'

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

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

Package suggested but not available for checking: ‘magick’

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

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

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

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 suggested but not available for checking:
  'readxl', 'testthat', 'purrr'
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
Packages required but not available: 'dplyr', 'purrr', 'tidyr', 'stringr'

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:
  > # Required packages for testing
  > suppressMessages({
  +   library(testthat)
  +   library(merlin)
  +   library(nlme)
  +   library(survival)
  + })
  Error in library(testthat) : there is no package called 'testthat'
  Calls: suppressMessages -> withCallingHandlers -> library
  Execution halted
Packages required but not available: 'ggpubr', 'progress'

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

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

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', 'tidyr'

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', 'patchwork', 'progress'

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

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

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

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

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

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', 'piggyback', 'purrr', 'readr', '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:
  'tibble', 'usethis', 'dplyr', 'ggplot2', 'ggfittext', 'forcats',
  'ggimage', 'patchwork', 'stringr', 'tidyr', 'purrr', 'meta'

Packages suggested but not available for checking:
  'Rd2roxygen', 'kableExtra', 'downloadthis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'survminer', 'rms', 'tidyr', 'ggplot2', '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: 'C50', 'caret', 'webchem'

Packages suggested but not available for checking:
  'mixOmics', 'ropls', 'xcms'

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: 'factoextra', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'ggplot2', 'igraph', 'taxize', 'dplyr', 'readr',
  'ggfittext', 'cowplot', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'phyloseq', 'traits', 'DESeq2'

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

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

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

Packages suggested but not available for checking:
  'testthat', 'metaumbrella', 'TOSTER', 'epiR', 'meta', 'MetaUtility'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Packages suggested but not available for checking:
  'igraph', 'testthat', 'lme4', 'meta', 'netmeta', 'rms'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # to also run skip_on_cran() tests, uncomment:
  > #Sys.setenv(NOT_CRAN="true")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'magick', 'purrr'

Packages suggested but not available for checking: 'mockery', '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
Packages required but not available: 'caret', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape2’
Package required but not available: ‘ggplot2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'nloptr', 'Epi', 'glmmTMB', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ### to also run skip_on_cran() tests, uncomment:
  > #Sys.setenv(NOT_CRAN="true")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                           ^
checkRd: (-1) datagenerator.Rd:17: Lost braces; missing escapes or markup?
    17 | Returns data frame with \code{n*K} rows (if \code{n} is a scalar), or \code{sum(n)} rows (if \code{n} is a \code{K}-element vector). The data frame contains columns "y", "x1", \dots, "x_{p-1}" and "group" if \code{family="gaussian"}, \code{"binomial"} or \code{"poisson"}; or contains columns "time", "status", "x1", \dots, "x_{p-1}" and "group" if \code{family="cox"}.
       |                                                                                                                                                                                                                                                                                                                                        ^
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'roxygen2', 'devtools', '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', 'ggplot2', 'ggrepel', 'purrr', 'stringr', 'tibble', 'tidyr',
  'viridis'

Package suggested but not available for checking: ‘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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'meta', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) asympVar_LinReg.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'stringr', 'GEOquery', 'GEOmetadb', 'RSQLite', 'ggpubr',
  'manhattanly', 'dplyr', 'reshape2', 'AnnotationDbi', 'readr',
  'plotly'

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

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

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

--- re-building ‘ar-grid.Rmd’ using rmarkdown

Quitting from lines 19-22 [unnamed-chunk-2] (ar-grid.Rmd)
Error: processing vignette 'ar-grid.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘ar-grid.Rmd’

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

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

--- re-building ‘mockup-table.Rmd’ using rmarkdown

Quitting from lines 21-24 [unnamed-chunk-2] (mockup-table.Rmd)
Error: processing vignette 'mockup-table.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘mockup-table.Rmd’

SUMMARY: processing the following files failed:
  ‘ar-grid.Rmd’ ‘mockup-table.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'devtools', 'ggplot2'
Packages required but not available: 'ggplot2', 'DESeq2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GEOquery', 'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db',
  'hgu133a.db', 'hgu95av2.db'
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: ‘progress’

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'reshape2', 'caret', 'tsibble'

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

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

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

Packages suggested but not available for checking:
  'stringr', 'Hmisc', 'ggraph', 'networkD3', 'ggpmisc', 'ggtree',
  'treeio', 'ggpubr'

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

Package suggested but not available for checking: ‘testthat’

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

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', 'GGally', 'ggforce', 'ggplot2', 'ggrepel', 'lme4',
  'lmerTest', 'patchwork', 'purrr', 'tibble', 'tidyr', 'tidyselect'

Package suggested but not available for checking: ‘roxygen2’

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'

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:
  'cowplot', 'dplyr', 'ggplot2', 'tidyr', '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:
  'dendextend', 'dplyr', 'ggforce', 'ggrepel', 'reshape2', 'stringr',
  'tidyverse'

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

Packages suggested but not available for checking: 'pimeta', 'robvis'

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

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DESeq2’
checkRd: (-1) param.Rd:29: Lost braces
    29 | T. Strub, S. Giuliano, T. Ye, et al. (2011) Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma. emph{Oncogene} \bold{30}:2319-32.
       |                                                                                                                                                                       ^
Packages suggested but not available for checking: 'semPlot', '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: ‘meta’

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

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

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', 'metacore', 'purrr', 'stringr', 'tidyr', 'tibble'

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: 'meta', 'readxl'

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

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

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

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

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: ‘ggplot2’

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

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

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

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

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', 'lubridate', 'purrr', 'stringr', 'tidyr', 'vctrs'

Packages suggested but not available for checking:
  'ggforce', '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
Packages required but not available: 'sqldf', 'dplyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
Found the following HTML validation problems:
BA.est.html:149:32 (BA.est.Rd:121): Warning: trimming empty <code>
Packages required but not available: 'dplyr', 'purrr'

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:
  > # 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', 'stringr', 'tibble', 'lubridate', 'tidyr'

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'RSQLite', 'ggpp'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gh', 'dplyr', 'lubridate', 'purrr', 'tidyr', 'googledrive',
  'googlesheets4', 'janitor', '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
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’

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

Packages suggested but not available for checking:
  'pkgdown', 'reshape2', 'testthat', 'viridis', 'vdiffr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'optimx', 'testthat', 'ggplot2', 'cowplot'
Packages required but not available: 'readr', 'stringr', 'tibble'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'devtools', 'ggplot2', 'dplyr', 'ggpubr', 'purrr',
  'patchwork', 'tidyr', 'lme4', 'lmerTest', 'tidyverse'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dendextend', 'FactoMineR', 'ggplot2', 'ggrepel', 'Hmisc',
  'patchwork', 'reshape2', 'rstatix'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pkgdown’
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'
Package suggested but not available for checking: ‘dataRetrieval’
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'reshape2'
'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 ‘Discriminability.Rmd’ using rmarkdown

Quitting from lines 17-33 [unnamed-chunk-1] (Discriminability.Rmd)
Error: processing vignette 'Discriminability.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘Discriminability.Rmd’

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

Quitting from lines 13-50 [unnamed-chunk-1] (MGC.Rmd)
Error: processing vignette 'MGC.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘MGC.Rmd’

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

Quitting from lines 40-42 [unnamed-chunk-3] (class_simulations.Rmd)
Error: processing vignette 'class_simulations.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building ‘class_simulations.Rmd’

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

Quitting from lines 64-69 [unnamed-chunk-3] (dep_simulations.Rmd)
Error: processing vignette 'dep_simulations.Rmd' failed with diagnostics:
object 'geom_line' not found
--- failed re-building ‘dep_simulations.Rmd’

SUMMARY: processing the following files failed:
  ‘Discriminability.Rmd’ ‘MGC.Rmd’ ‘class_simulations.Rmd’
  ‘dep_simulations.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'gamm4', 'viridis', '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: ‘ggplot2’
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
checkRd: (-1) calcQuantiles.Rd:52: Lost braces; missing escapes or markup?
    52 | {M/F}\emph{Mean}(patchNum).csv and {M/F}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) calcQuantiles.Rd:52: Lost braces; missing escapes or markup?
    52 | {M/F}\emph{Mean}(patchNum).csv and {M/F}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                    ^
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
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 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', 'reshape2', '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
Packages required but not available: 'stringr', 'Hmisc', 'qgraph'

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’
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
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', '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: 'ggplot2', 'dplyr', 'caret'

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.
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’
Running ‘testthat.R’ [0s/1s]
Running 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’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Mhorseshoe.Rmd’ using rmarkdown

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

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

Error: Vignette re-building failed.
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 suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'imp4p', 'mice', 'stringr'

Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'

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: 'pcalg', 'mice'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'BIFIEsurvey', 'blme', 'car', 'lme4', 'MBESS', 'mdmb', 'readxl',
  'synthpop'

Packages which this enhances but not available for checking:
  'imputeR', 'jomo', 'micemd', 'mitml', 'simputation'

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

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: ‘systemfit’

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

Package suggested but not available for checking: ‘AER’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'mice', 'ggplot2', 'UpSetR', 'dplyr'
Specified C++11: please drop specification unless essential
checkRd: (-1) VIF.Rd:47: Lost braces; missing escapes or markup?
    47 | vif_corrected = vif_basic^{(1/(2*df))}
       |                           ^
Running examples in ‘miceFast-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare_imp
> ### Title: Comparing imputations and original data distributions
> ### Aliases: compare_imp
> 
> ### ** Examples
> 
> library(miceFast)
> 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘miceFast-intro.Rmd’ using rmarkdown

Quitting from lines 21-23 [unnamed-chunk-1] (miceFast-intro.Rmd)
Error: processing vignette 'miceFast-intro.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building ‘miceFast-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘miceFast-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'mice', 'lme4', 'jomo', 'GJRM'

Packages suggested but not available for checking:
  'VIM', 'ggplot2', 'broom.mixed'

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

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', 'mitml', 'tidyr'

Packages suggested but not available for checking:
  'broom.mixed', 'furrr', 'haven', 'lme4', 'miceadds', 'purrr',
  'rstan', 'testthat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'MVN', 'testthat', 'roxygen2', 'devtools'
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2016 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘paper.Rnw’ using knitr

Quitting from lines 341-342 [sunspot3] (paper.Rnw)
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘paper.Rnw’

--- re-building ‘tolatex-examples.Rnw’ using knitr
--- finished re-building ‘tolatex-examples.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available:
  'dplyr', 'broom', 'phyloseq', 'ggplot2', 'ggpubr', 'DESeq2',
  'rstatix', 'tidyr', 'phangorn'

Packages suggested but not available for checking: 'dada2', 'testthat'

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

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

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

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

Package suggested but not available for checking: ‘microcontax.data’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggh4x', 'ggplot2', 'ggthemes', 'purrr', 'rstatix',
  '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', 'tibble', 'ggplot2', 'reshape2', 'igraph'

Packages suggested but not available for checking:
  'GUniFrac', 'ggpubr', 'ggdendro', 'ggrepel', 'rgexf', 'mice',
  'GGally'

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

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', 'rmapshaper', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'readr'
Running ‘testthat.R’ [0s/1s]
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 ‘Advanced.Rmd’ using rmarkdown
--- finished re-building ‘Advanced.Rmd’

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

Quitting from lines 18-22 [setup] (BH_aqua.Rmd)
Error: processing vignette 'BH_aqua.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘BH_aqua.Rmd’

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

Quitting from lines 18-22 [setup] (BQ_mosquito.Rmd)
Error: processing vignette 'BQ_mosquito.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘BQ_mosquito.Rmd’

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

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

Quitting from lines 18-22 [setup] (MOI_human.Rmd)
Error: processing vignette 'MOI_human.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘MOI_human.Rmd’

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

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

Quitting from lines 18-22 [setup] (RM_mosquito.Rmd)
Error: processing vignette 'RM_mosquito.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘RM_mosquito.Rmd’

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

Quitting from lines 18-22 [setup] (RM_transmission.Rmd)
Error: processing vignette 'RM_transmission.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘RM_transmission.Rmd’

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

SUMMARY: processing the following files failed:
  ‘BH_aqua.Rmd’ ‘BQ_mosquito.Rmd’ ‘MOI_human.Rmd’ ‘RM_mosquito.Rmd’
  ‘RM_transmission.Rmd’

Error: Vignette re-building failed.
Execution halted
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 ‘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:
  'microseq', 'dplyr', 'stringr', 'igraph', 'tibble'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) RNGStream.Rd:29: Lost braces
    29 | item{open}{function to use the current seed}
       |     ^
checkRd: (-1) RNGStream.Rd:29: Lost braces
    29 | item{open}{function to use the current seed}
       |           ^
checkRd: (-1) RNGStream.Rd:30: Lost braces
    30 | item{close}{function to make the current seed equal to .Random.seed}
       |     ^
checkRd: (-1) RNGStream.Rd:30: Lost braces
    30 | item{close}{function to make the current seed equal to .Random.seed}
       |            ^
checkRd: (-1) RNGStream.Rd:31: Lost braces
    31 | item{resetStream}{function to move back to start of stream}
       |     ^
checkRd: (-1) RNGStream.Rd:31: Lost braces
    31 | item{resetStream}{function to move back to start of stream}
       |                  ^
checkRd: (-1) RNGStream.Rd:32: Lost braces
    32 | item{resetSubStream}{function to move back to start of sub-stream}
       |     ^
checkRd: (-1) RNGStream.Rd:32: Lost braces
    32 | item{resetSubStream}{function to move back to start of sub-stream}
       |                     ^
checkRd: (-1) RNGStream.Rd:33: Lost braces
    33 | item{nextSubStream}{function to move to next sub-stream}
       |     ^
checkRd: (-1) RNGStream.Rd:33: Lost braces
    33 | item{nextSubStream}{function to move to next sub-stream}
       |                    ^
checkRd: (-1) RNGStream.Rd:34: Lost braces
    34 | item{nextStream}{function to move to next stream}
       |     ^
checkRd: (-1) RNGStream.Rd:34: Lost braces
    34 | item{nextStream}{function to move to next stream}
       |                 ^
Package required but not available: ‘vctrs’

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

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

Packages suggested but not available for checking:
  'AER', 'sampleSelection', 'mlogit'

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: 'caret', 'genefilter'

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.
Package required but not available: ‘lubridate’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mice.impute.midastouch
> ### Title: Predictive Mean Matching with distance aided selection of donors
> ### Aliases: mice.impute.midastouch midastouch
> ### Keywords: mice
> 
> ### ** Examples
> 
> ## from R:: mice, slightly adapted ##
> 
> # do default multiple imputation on a numeric matrix
> library(midastouch)
> library(mice)
Error in library(mice) : there is no package called ‘mice’
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', 'mice', 'midfielddata'
Error(s) in re-building vignettes:
  ...
--- re-building ‘art-010-planning.Rmd’ using rmarkdown

Quitting from lines 23-57 (art-010-planning.Rmd)
Error: processing vignette 'art-010-planning.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘art-010-planning.Rmd’

--- re-building ‘art-040-programs.Rmd’ using rmarkdown

Quitting from lines 24-43 (art-040-programs.Rmd)
Error: processing vignette 'art-040-programs.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘art-040-programs.Rmd’

SUMMARY: processing the following files failed:
  ‘art-010-planning.Rmd’ ‘art-040-programs.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'plotly', '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
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'mice', 'dplyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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', 'tidyr', 'stringr', 'tibble', 'forcats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'manynet', 'dplyr', 'ggplot2', 'igraph', 'network', 'furrr',
  'pillar', 'purrr', 'sna', 'tidygraph', 'tidyr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'igraph', 'ggplot2'
Specified C++14: please drop specification unless essential
checkRd: (-1) discretizeMutual.Rd:58: Lost braces
    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                      ^
checkRd: (-1) discretizeMutual.Rd:58: Lost braces
    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                                      ^
checkRd: (-1) discretizeMutual.Rd:58: Lost braces
    58 | \item{two vectors containing the cutpoints for each variable : \emph{cutpoints1} corresponds to /emph{myDist1}, /emph{cutpoints2} corresponds to /emph{myDist2}.}
       |                                                                                                                                                       ^
checkRd: (-1) discretizeMutual.Rd:62: Lost braces
    62 | \item{if $emph{plot} == TRUE, a plot object (requires ggplot2 and gridExtra).}
       |               ^
checkRd: (-1) miic.Rd:158-209: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) miic.Rd:211: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) miic.Rd:213-214: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘mice’

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

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.
Packages required but not available: 'caret', 'dplyr'

Packages suggested but not available for checking:
  'forcats', 'furrr', 'ggplot2', 'progress', 'purrr', 'rsample',
  'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid NAMESPACE file, parsing gives:
Error in loadNamespace(name): there is no package called ‘testthat’

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Packages required but not available:
  'dplyr', 'pillar', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'gurobi', '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:
  'testthat', 'Hmisc', 'ggplot2'
Specified C++11: please drop specification unless essential
checkRd: (-1) milr.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milr.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require(pipeR)
  Loading required package: pipeR
  > library("milr")
  > test_check("milr")
  Error in test_check("milr") : could not find function "test_check"
  Execution halted
Packages required but not available:
  'dplyr', 'fuzzyjoin', 'stringr', 'tidyr', 'testthat', 'reshape2'

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:
  'caret', 'ggplot2', 'heatmaply', 'plotly', 'purrr', 'shinyFiles',
  'survminer', 'dplyr'

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

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

Package suggested but not available for checking: ‘kableExtra’

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

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.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'InteractiveComplexHeatmap', 'dplyr', 'hms'

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', 'testthat', 'mockery', 'testthis', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'purrr', 'testthat', 'tidyr', '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 ‘Writing-vignettes-with-minidown.Rmd’ using rmarkdown
Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
  number of items to replace is not a multiple of replacement length
Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
  number of items to replace is not a multiple of replacement length

Quitting from lines 122-155 [render-size] (Writing-vignettes-with-minidown.Rmd)
Error: processing vignette 'Writing-vignettes-with-minidown.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘Writing-vignettes-with-minidown.Rmd’

SUMMARY: processing the following file failed:
  ‘Writing-vignettes-with-minidown.Rmd’

Error: Vignette re-building failed.
Execution halted
'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: 'meta', 'colourpicker', 'readxl'

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
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’
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’
Packages suggested but not available for checking: 'testthat', 'pkgdown'
Running ‘testthat.R’ [0s/1s]
Running 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', 'hms', 'readr'
File ‘minty/libs/minty.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
checkRd: (-1) gof.estimates.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gof.estimates.Rd:63-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gof.estimates.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:63-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:92-95: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'ggplot2', 'stringr', 'tidyr', 'readxl', 'shiny.i18n', 'readr',
  'dplyr', 'reshape2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sim.data.Rd:11: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:12: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:13: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) sim.data.Rd:27: Lost braces in \enumerate; meant \describe ?
Packages required but not available: 'rstan', 'dirichletprocess'

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', 'plotly', 'purrr', 'readr', 'readxl',
  'stringr', 'textclean', 'tidyr', 'tidytext'

Packages suggested but not available for checking:
  'kableExtra', 'reshape2', 'testthat'

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

Package suggested but not available for checking: ‘kableExtra’

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: 'globaltest', 'GlobalAncova'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘nloptr’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mice’
Error(s) in re-building vignettes:
  ...
--- re-building ‘misaem.Rmd’ using rmarkdown

Quitting from lines 60-68 [unnamed-chunk-3] (misaem.Rmd)
Error: processing vignette 'misaem.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building ‘misaem.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘R2jags’

Package suggested but not available for checking: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'phyloseq', 'ggplot2', 'dada2', 'dplyr', 'purrr'

Packages suggested but not available for checking:
  'adespatial', 'ANCOMBC', 'ComplexUpset', 'DESeq2', 'devtools',
  'ggalluvial', 'ggfittext', 'gghalves', 'ggh4x', 'ggstatsplot',
  'ggridges', 'ggVennDiagram', 'gtsummary', 'iNEXT', 'metacoder',
  'mia', 'mixtools', 'networkD3', 'patchwork', 'phangorn',
  'phyloseqGraphTest', 'plotly', 'reshape2', 'rotl', 'stringr',
  'testthat', 'tibble', 'tidyr', 'treemapify', 'vctrs', 'viridis'

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

Package suggested but not available for checking: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Ecdat’
checkRd: (-1) sumKeepAttr.Rd:19: Lost braces
    19 |       (only relevant if code{x} has only one element).}
       |                             ^
Running examples in ‘miscTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: colMedians
> ### Title: Medians of Columns
> ### Aliases: colMedians
> ### Keywords: array
> 
> ### ** Examples
> 
>    data( "Electricity", package = "Ecdat" )
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘Ecdat’
Calls: data -> find.package
Execution halted
Running ‘colMediansTest.R’ [0s/0s]
  Running ‘ddnormTest.R’ [0s/1s]
  Comparing ‘ddnormTest.Rout’ to ‘ddnormTest.Rout.save’ ... OK
  Running ‘insertColRow.R’ [0s/0s]
  Comparing ‘insertColRow.Rout’ to ‘insertColRow.Rout.save’ ... OK
  Running ‘lmMethods.R’ [0s/1s]
  Comparing ‘lmMethods.Rout’ to ‘lmMethods.Rout.save’ ... OK
  Running ‘margEffTest.R’ [0s/0s]
  Comparing ‘margEffTest.Rout’ to ‘margEffTest.Rout.save’ ... OK
  Running ‘semidefTest.R’ [0s/1s]
  Comparing ‘semidefTest.Rout’ to ‘semidefTest.Rout.save’ ... OK
  Running ‘stdErTests.R’ [0s/1s]
  Comparing ‘stdErTests.Rout’ to ‘stdErTests.Rout.save’ ... OK
  Running ‘sumKeepAttrTest.R’ [0s/1s]
  Comparing ‘sumKeepAttrTest.Rout’ to ‘sumKeepAttrTest.Rout.save’ ... OK
  Running ‘summarizeDF_tests.R’ [0s/1s]
  Comparing ‘summarizeDF_tests.Rout’ to ‘summarizeDF_tests.Rout.save’ ... OK
Running the tests in ‘tests/colMediansTest.R’ failed.
Complete output:
  > library( "miscTools" )
  > 
  > 
  > ## matrix
  > m <- matrix( 1:24, nrow = 6, ncol = 4 )
  > 
  > cm1 <- colMedians( m )
  > print( cm1 )
  [1]  3.5  9.5 15.5 21.5
  > 
  > rm1 <- rowMedians( m )
  > print( rm1 )
  [1] 10 11 12 13 14 15
  > 
  > all.equal( cm1, rowMedians( t( m ) ) )
  [1] TRUE
  > all.equal( rm1, colMedians( t( m ) ) )
  [1] TRUE
  > 
  > 
  > ## data.frame
  > data( "Electricity", package = "Ecdat" )
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'Ecdat'
  Calls: data -> find.package
  Execution halted
Packages suggested but not available for checking: 'mice', 'testthat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘miselect.Rmd’ using rmarkdown

Quitting from lines 76-82 [unnamed-chunk-4] (miselect.Rmd)
Error: processing vignette 'miselect.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building ‘miselect.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'plotly', 'dplyr', 'highcharter', 'tidyr', 'tidyverse', 'purrr',
  'patchwork', 'reshape2', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'dplyr', 'ggdendro', 'ggplot2', 'Hmisc', 'mi', 'mice', 'missMDA',
  'tidyr', 'VIM'

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: 'factoextra', 'ggplot2', 'sparsevar'

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

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

Package suggested but not available for checking: ‘mice’

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

Quitting from lines 103-113 [unnamed-chunk-2] (missForestPredict_convergence_criteria_and_error_monitoring.Rmd)
Error: processing vignette 'missForestPredict_convergence_criteria_and_error_monitoring.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘missForestPredict_convergence_criteria_and_error_monitoring.Rmd’

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

Quitting from lines 214-234 [unnamed-chunk-12] (missForestPredict_usage.Rmd)
Error: processing vignette 'missForestPredict_usage.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘missForestPredict_usage.Rmd’

SUMMARY: processing the following files failed:
  ‘missForestPredict_convergence_criteria_and_error_monitoring.Rmd’
  ‘missForestPredict_usage.Rmd’

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

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

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

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

Quitting from lines 52-65 [setup] (Generating-missing-values.Rmd)
Error: processing vignette 'Generating-missing-values.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Generating-missing-values.Rmd’

SUMMARY: processing the following file failed:
  ‘Generating-missing-values.Rmd’

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

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', 'nloptr', 'ggplot2', 'sbm'

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: ‘ggplot2’
Running examples in ‘mistr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QQplotgg
> ### Title: Implementation of Quantile-Quantile Plot with ggplot2
> ### Aliases: QQplotgg QQplotgg.default QQplotgg.dist QQnormgg
> 
> ### ** Examples
> 
> # sample vs sample
> QQplotgg(r(normdist(), 10000), r(tdist(df = 4), 10000))
Error: Package ggplot2 needed for this function to work. Please install it.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mistr-extensions.Rmd’ using rmarkdown

Quitting from lines 180-184 [unnamed-chunk-7] (mistr-extensions.Rmd)
Error: processing vignette 'mistr-extensions.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘mistr-extensions.Rmd’

--- re-building ‘mistr-introduction.Rmd’ using rmarkdown

Quitting from lines 212-214 [unnamed-chunk-12] (mistr-introduction.Rmd)
Error: processing vignette 'mistr-introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘mistr-introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘mistr-extensions.Rmd’ ‘mistr-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'haven', 'lme4', 'readxl'

Package suggested but not available for checking: ‘patchwork’

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

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

Packages suggested but not available for checking:
  'mice', 'miceadds', 'lme4', 'geepack', 'glmmTMB'

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:
  'clustree', 'karyoploteR', 'plotly', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) PV.Rd:14: Lost braces
    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
Packages required but not available: 'dplyr', 'igraph', 'stringr', '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', 'animation'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'Hmisc', 'purrr', 'tidyr'

Packages suggested but not available for checking:
  'GGally', 'mice', '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 suggested but not available for checking: 'fma', 'testthat'
Running examples in ‘mixAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MixARGaussian-class
> ### Title: mixAR models with Gaussian noise components
> ### Aliases: MixARGaussian-class MixARGaussian
> ### Keywords: classes MixAR
> 
> ### ** Examples
> 
> showClass("MixARGaussian")
Class "MixARGaussian" [package "mixAR"]

Slots:
                                                             
Name:        prob      order      shift      scale     arcoef
Class:    numeric    numeric    numeric    numeric raggedCoef

Extends: "MixAR"
> 
> ## load ibm data from BJ
> ## data(ibmclose, package = "fma")
> 
> ## compute a predictive density, assuming exampleModels$WL_ibm model
> ## for the first date after the end of the data
> pdf1 <- mix_pdf(exampleModels$WL_ibm, xcond = as.numeric(fma::ibmclose))
Error in (function (cond)  : 
  error in evaluating the argument 'xcond' in selecting a method for function 'mix_pdf': there is no package called ‘fma’
Calls: mix_pdf ... 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
Package required but not available: ‘nloptr’

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: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'tibble', 'purrr', 'dplyr', 'ggplot2', 'tidyr'
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: ‘latentcor’

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: ‘FrF2’
Running examples in ‘MixedLevelRSDs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QualRSD
> ### Title: Second Order RSDs with qualitative factors
> ### Aliases: QualRSD
> 
> ### ** Examples
> 
> library(MixedLevelRSDs)
> QualRSD(5,2, Interaction = FALSE )
Error in loadNamespace(x) : there is no package called ‘FrF2’
Calls: QualRSD ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'purrr', 'ggplot2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Packages required but not available: 'rstan', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) u4_cba_cor.Rd:35: Lost braces
    35 |   \code{t * 1} and \code{B} is of dimension{t * N}. Ideally, \code{fun.sim}()
       |                                            ^
Packages required but not available: 'ggplot2', 'mice', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Running ‘testthat.R’ [0s/1s]
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 ‘BasicGenetics.Rmd’ using rmarkdown
--- finished re-building ‘BasicGenetics.Rmd’

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

Quitting from lines 20-22 [load] (DistributionBuildingNComparison.Rmd)
Error: processing vignette 'DistributionBuildingNComparison.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘DistributionBuildingNComparison.Rmd’

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

Quitting from lines 20-22 [load package] (HypothesisTest.Rmd)
Error: processing vignette 'HypothesisTest.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘HypothesisTest.Rmd’

SUMMARY: processing the following files failed:
  ‘DistributionBuildingNComparison.Rmd’ ‘HypothesisTest.Rmd’

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

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

Package suggested but not available for checking: ‘lme4’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr'
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 ‘discriminant-analysis.Rmd’ using rmarkdown
--- finished re-building ‘discriminant-analysis.Rmd’

--- re-building ‘matrix-t-estimation.Rmd’ using rmarkdown

Quitting from lines 271-317 [dftenexample] (matrix-t-estimation.Rmd)
Error: processing vignette 'matrix-t-estimation.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘matrix-t-estimation.Rmd’

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

--- re-building ‘mixturemodel.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MixMatrix.Rcheck/vign_test/MixMatrix/vignettes/mixturemodel_files/figure-html/demo-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4451 bytes
Input file size = 5309 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3880
  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 = 3880

Output IDAT size = 3880 bytes (571 bytes decrease)
Output file size = 3958 bytes (1351 bytes = 25.45% decrease)

--- finished re-building ‘mixturemodel.Rmd’

SUMMARY: processing the following file failed:
  ‘matrix-t-estimation.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘meta’
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
Packages required but not available: 'ggplot2', 'patchwork'

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

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

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

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.
Packages required but not available:
  'ggplot2', 'R2jags', 'reshape2', 'ggmcmc', 'loo', 'bayesplot'

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: ‘plotly’

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', 'ggplot2', 'tidyr'

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

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

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

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', 'ggplot2', 'ggrepel', 'lubridate', 'plotly', 'progress',
  'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bamlss', 'gamm4', 'refund', 'fdapace', 'sparseFLMM'

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

Package suggested but not available for checking: ‘mice’

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

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

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', 'mockery'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(data.table)
  + })
  Error in library(testthat) : there is no package called 'testthat'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
Packages required but not available:
  'ggplot2', 'MKdescr', 'MKinfer', 'qqplotr'

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

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', 'gt', 'magick'

Packages suggested but not available for checking:
  'dplyr', 'ggtext', 'gridtext', 'sjmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
Packages required but not available: 'igraph', 'GRIDCOPULA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ConfusionTableR', 'dplyr', 'parsnip', 'rsample', 'recipes',
  'workflows', 'caret', 'OddsPlotty', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) mldrGUI.Rd:22-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mldrGUI.Rd:32-34: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
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) real2canon.rd:9: Lost braces; missing escapes or markup?
     9 |       (2) All x-coordinates of R1',..,Rn' are distinct, and take values in {1,..,2n}.
       |                                                                            ^
checkRd: (-1) real2canon.rd:10: Lost braces; missing escapes or markup?
    10 |       (3) All y-coordinates of R1',..,Rn' are distinct, and take values in {1,..,2n}.
       |                                                                            ^
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Packages required but not available:
  'ergm', 'network', 'stringr', 'GGally', 'ggplot2', 'cowplot',
  'reshape2', 'sna'

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: ‘ggplot2’

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

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

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

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

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:
  'keras', 'sparklyr', 'testthat'

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

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 required but not available: ‘lme4’

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: 'kdry', 'mlexperiments'

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

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

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 suggested but not available for checking: 'bootImpute', 'testthat'
checkRd: (-1) refBasedCts.Rd:44: Lost braces
    44 | using reference based imputation as proposed by \doi{10.1080/10543406.2013.834911}{Carpenter et al (2013)}. This approach
       |                                                                                   ^
Running ‘testthat.R’ [0s/1s]
Running 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:
  'minfi', 'GEOquery', 'IlluminaHumanMethylation450kmanifest'
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: 'lme4', 'lmerTest', 'varTestnlme'

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: 'lme4', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'TSclust', 'forecast', 'tsfeatures', 'ggplot2', 'fda.usc', 'TSdist',
  'DescTools', 'ClusterR', 'AID', 'caret', 'igraph'

Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8', 'testthat'

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

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

Packages suggested but not available for checking: 'car', 'AER', '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 suggested but not available for checking: 'progress', 'C50'
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'lme4', 'lmerTest', 'simr', 'tidyr'

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: ‘batchtools’

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: 'ClusterR', 'testthat'
Packages suggested but not available for checking:
  'RSQLite', 'dbplyr', 'dplyr', 'testthat', 'tibble'
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'patchwork', 'mlr3viz', 'kableExtra', 'iml'

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

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:
  'caret', 'FSelectorRcpp', 'testthat'
Package suggested but not available for checking: ‘testthat’
Running examples in ‘mlr3fselect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract_inner_fselect_archives
> ### Title: Extract Inner Feature Selection Archives
> ### Aliases: extract_inner_fselect_archives
> 
> ### ** Examples
> 
> # Nested Resampling on Palmer Penguins Data Set
> 
> # create auto fselector
> at = auto_fselector(
+   fselector = fs("random_search"),
+   learner = lrn("classif.rpart"),
+   resampling = rsmp ("holdout"),
+   measure = msr("classif.ce"),
+   term_evals = 4)
> 
> resampling_outer = rsmp("cv", folds = 2)
> rr = resample(tsk("penguins"), at, resampling_outer, store_models = TRUE)
Error in as.data.table(palmerpenguins::penguins) : 
  cannot return a promise (PROMSXP) object
Calls: resample ... dictionary_initialize_item -> do.call -> <Anonymous> -> as.data.table
Execution halted
Package suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking: 'kknn', 'testthat'
Packages suggested but not available for checking: 'nloptr', 'testthat'
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
File ‘mlr3misc/libs/mlr3misc.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 suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking:
  'ggplot2', 'igraph', 'lme4', 'nloptr', 'testthat', 'bestNormalize',
  'smotefamily', 'NMF', 'kknn'
Running examples in ‘mlr3pipelines-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlr_pipeops_imputelearner
> ### Title: Impute Features by Fitting a Learner
> ### Aliases: mlr_pipeops_imputelearner PipeOpImputeLearner
> 
> ### ** Examples
> 
> ## Don't show: 
>  if (requireNamespace("rpart")) { 
+ ## End(Don't show)
+ library("mlr3")
+ 
+ task = tsk("pima")
+ task$missings()
+ 
+ po = po("imputelearner", lrn("regr.rpart"))
+ new_task = po$train(list(task = task))[[1]]
+ new_task$missings()
+ 
+ # '$state' of the "regr.rpart" Learner, trained to predict the 'mass' column:
+ po$state$model$mass
+ 
+ library("mlr3learners")
+ # to use the "regr.kknn" Learner, prefix it with its own imputation method!
+ # The "imputehist" PipeOp is used to train "regr.kknn"; predictions of this
+ # trained Learner are then used to impute the missing values in the Task.
+ po = po("imputelearner",
+   po("imputehist") %>>% lrn("regr.kknn")
+ )
+ 
+ new_task = po$train(list(task = task))[[1]]
+ new_task$missings()
+ 
+ ## Don't show: 
+  } 
Warning: Package 'kknn' required but not installed for Learner 'regr.kknn'
Warning: Package 'kknn' required but not installed for Learner 'imputehist.regr.kknn'
Error: The following packages could not be loaded: kknn
This happened PipeOp imputelearner's $train()
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
mlr_pipeops    4.792  0.063   8.150
mlr_graphs_ovr 4.296  0.002   7.068
Package suggested but not available for checking: ‘testthat’
Running examples in ‘mlr3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BenchmarkResult
> ### Title: Container for Benchmarking Results
> ### Aliases: BenchmarkResult
> 
> ### ** Examples
> 
> set.seed(123)
> learners = list(
+   lrn("classif.featureless", predict_type = "prob"),
+   lrn("classif.rpart", predict_type = "prob")
+ )
> 
> design = benchmark_grid(
+   tasks = list(tsk("sonar"), tsk("penguins")),
+   learners = learners,
+   resamplings = rsmp("cv", folds = 3)
+ )
Error in as.data.table(palmerpenguins::penguins) : 
  cannot return a promise (PROMSXP) object
Calls: benchmark_grid ... dictionary_initialize_item -> do.call -> <Anonymous> -> as.data.table
Execution halted
Packages suggested but not available for checking: 'animint2', 'testthat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ResamplingSameOtherCV.Rmd’ using rmarkdown
--- finished re-building ‘ResamplingSameOtherCV.Rmd’

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

Quitting from lines 36-52 [simulationScatter] (ResamplingSameOtherSizesCV.Rmd)
Error: processing vignette 'ResamplingSameOtherSizesCV.Rmd' failed with diagnostics:
there is no package called 'animint2'
--- failed re-building ‘ResamplingSameOtherSizesCV.Rmd’

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

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

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

Packages suggested but not available for checking:
  'testthat', 'shinytest', 'devtools', 'igraph', 'readxl', 'DALEX',
  'DALEXtra', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'bench', 'testthat'
Running examples in ‘mlr3spatial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict_spatial
> ### Title: Predict on Spatial Objects with mlr3 Learners
> ### Aliases: predict_spatial
> 
> ### ** Examples
> 
> library(terra, exclude = "resample")
terra 1.7.78
> 
> # fit rpart on training points
> task_train = tsk("leipzig")
Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir,  : 
  package tibble not available: install first?
Calls: tsk ... st_read -> st_read.character -> process_cpl_read_ogr
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'caret', 'CAST', 'ggsci', 'ggtext', 'patchwork', 'plotly',
  'sperrorest', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'iml', 'mlr3fairness'
Running examples in ‘mlr3summary-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.Learner
> ### Title: Summarizing mlr3 Learners
> ### Aliases: summary.Learner summary.GraphLearner print.summary.Learner
> 
> ### ** Examples
> 
> if (require("mlr3")) {
+   tsk_iris = tsk("iris")
+   lrn_rpart =  lrn("classif.rpart", predict_type = "prob")
+   lrn_rpart$train(task = tsk_iris)
+   rsmp_cv3 = rsmp("cv", folds = 3L)
+   rr = resample(tsk_iris, lrn_rpart, rsmp_cv3, store_model = TRUE)
+   summary(lrn_rpart, rr)
+ }
Loading required package: mlr3
INFO  [15:59:38.941] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/3)
INFO  [15:59:39.084] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 2/3)
INFO  [15:59:39.192] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 3/3)
Error: Package 'iml' needed for this function to work. Please install it.
Execution halted
Packages suggested but not available for checking: 'nloptr', 'testthat'
Running examples in ‘mlr3tuning-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AutoTuner
> ### Title: Class for Automatic Tuning
> ### Aliases: AutoTuner
> 
> ### ** Examples
> 
> # Automatic Tuning
> 
> # split to train and external set
> task = tsk("penguins")
Error in as.data.table(palmerpenguins::penguins) : 
  cannot return a promise (PROMSXP) object
Calls: tsk ... dictionary_initialize_item -> do.call -> <Anonymous> -> as.data.table
Execution halted
Packages suggested but not available for checking: 'kknn', 'testthat'
Package required but not available: ‘mlr3viz’

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

Packages suggested but not available for checking:
  'GGally', 'ggdendro', 'ggfortify', 'ggparty', 'patchwork', 'precrec',
  'testthat', 'vdiffr'

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

Packages suggested but not available for checking:
  'testthat', 'mRMRe', 'randomForestSRC', 'FSelectorRcpp', 'Hmisc'

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

Packages suggested but not available for checking:
  'cmaesr', 'ggplot2', 'GGally', 'kknn', 'reshape2', 'testthat'

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

Packages suggested but not available for checking:
  'adabag', 'batchtools', 'C50', 'caret', 'ClusterR', 'cowplot',
  'Cubist', 'fda.usc', 'forecast', 'FSelectorRcpp', 'ggpubr', 'Hmisc',
  'kknn', 'klaR', 'mlrMBO', 'mmpf', 'mRMRe', 'pec', 'refund', 'smoof',
  'survAUC', 'SwarmSVM', 'testthat', 'tidyr', 'tsfeatures', 'vdiffr'

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:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tidyr', 'stringr', 'opalr', 'fabR', 'madshapR'

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

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

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

Packages suggested but not available for checking: 'AER', 'tram', 'rms'

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
Package required but not available: ‘nloptr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'arm', 'qgraph', 'dplyr', 'MplusAutomation', 'graphicalVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggforce', 'cowplot', 'reshape2', 'dplyr'
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 ‘vignette.Rmd’ using rmarkdown

Quitting from lines 76-81 [generic] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Please install ggplot2: install.packages('ggplot2')
--- 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: ‘ggplot2’

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', 'ggplot2', 'reshape2'

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: 'mma', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mosaic', 'mosaicCalc'
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
File ‘mmap/libs/mmap.so’:
  Found non-API calls to R: ‘SET_ENCLOS’, ‘SET_FRAME’, ‘SET_HASHTAB’

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:
  'lubridate', 'ggplot2', 'dplyr', 'stringr', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'refund', 'dplyr', 'tidyr', 'cosinor', 'cosinor2', 'accelerometry',
  'ActCR', 'ActFrag', 'kableExtra', 'GGIR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'testthat', 'caret', 'ggplot2', 'ggpubr', 'cowplot'
'LazyData' is specified without a 'data' directory
Running ‘helpers.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 ‘Cluster-Analysis.rmd’ using rmarkdown

Quitting from lines 26-95 [unnamed-chunk-1] (Cluster-Analysis.rmd)
Error: processing vignette 'Cluster-Analysis.rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Cluster-Analysis.rmd’

SUMMARY: processing the following file failed:
  ‘Cluster-Analysis.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 required but not available: 'testthat', 'psqn'

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', 'devtools', 'roxygen2', 'qtl2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MMD_attr.Rd:62: Lost braces; missing escapes or markup?
    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) mmeln.Rd:69: Lost braces; missing escapes or markup?
    69 |   \item{obj$M}{Number of total observations sum_{i=1}^N(pi)}
       |                                                 ^
Packages required but not available: 'lme4', 'stringr'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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: 'geepack', 'testthat'
Packages required but not available: 'Spectrum', 'igraph'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) average.fit.models.Rd:6: Lost braces; missing escapes or markup?
     6 | These function takes the output of pgls.iter and uses its list of objects { model fits, optimzations (e.g.AICc)} and performs a weighted average on the ctoefficients estimated in the former by weighting by the latter. The parameters can also optionally be converted to binary by specifying "binary=FALSE" or just running the alias wraper function for assessing evidence of variable importance (Burnham & Anderson 2000).
       |                                                                           ^
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.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
checkRd: (-1) k2d.Rd:26: Lost braces
    26 | d_ND(x,y) = sqrt{ k(x,x) - 2k(x,y) + k(y,y)}.
       |                 ^
checkRd: (-1) k2d.Rd:34: Lost braces
    34 | d_n(x,y) = 1 - k(x,y)/sqrt{ k(x,x)k(y,y)},
       |                           ^
Package required but not available: ‘ggplot2’

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

Packages suggested but not available for checking:
  'car', 'dplyr', 'ggplot2', 'glmmTMB', 'hardhat', 'lme4', 'mockery',
  'parsnip', 'purrr', 'testthat', 'tidymodels'

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: ‘rio’

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'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘run-all.R’ [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: ‘flexsurv’

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

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

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', 'janitor', '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
Packages which this enhances but not available for checking:
  'aMNLFA', 'GPCMlasso'
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 ‘OVA_Predictions_For_MNL.Rmd’ using rmarkdown

Quitting from lines 78-89 [setup] (OVA_Predictions_For_MNL.Rmd)
Error: processing vignette 'OVA_Predictions_For_MNL.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘OVA_Predictions_For_MNL.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) mom.mtruncnorm.Rd:35: Lost braces
    35 |   \item{cum}{a logical value; if  code{TRUE}  (default value), cumulants 
       |                                       ^
checkRd: (-1) mom.mtruncnorm.Rd:43: Lost braces; missing escapes or markup?
    43 | The maximal value of {d} is \code{20}. If this threshold is exceeded, \code{NA}s
       |                      ^
checkRd: (-1) mt.Rd:110: Lost braces
   110 |   and code{tvpack}, downloaded in 2005 and again in 2007 from his webpage, 
       |           ^
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', 'ggplot2', 'tibble'

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:
  'caret', 'kableExtra', 'ggplot2', 'mailR'

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 suggested but not available for checking:
  'vcfR', 'biomaRt', 'optiSel', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
checkRd: (-1) creating.phenotypic.transform.Rd:20: Lost braces
    20 | trafo <- function(x){ return(x^2)}
       |                     ^
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'ggplot2', 'egg', 'tibble', '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: ‘sads’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyranges', 'dplyr', 'MultiAssayExperiment', 'stringr', 'ggbio',
  'AnnotationDbi', 'GenomicFeatures', 'ensembldb', 'ggplot2',
  'ggrepel', 'qvalue', 'tidyr', 'ggridges', 'tidyselect'

Packages suggested but not available for checking:
  'ArchR', 'RMariaDB', 'motifmatchr',
  'TxDb.Hsapiens.UCSC.hg38.refGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db', 'chromVAR',
  'testthat', 'glmmTMB', 'waldo', 'purrr', 'lmerTest', 'lme4',
  'cowplot', 'mixtools'

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

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

Quitting from lines 90-91 [create-package] (mockr.Rmd)
Error: processing vignette 'mockr.Rmd' failed with diagnostics:
there is no package called 'usethis'
--- failed re-building ‘mockr.Rmd’

SUMMARY: processing the following file failed:
  ‘mockr.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
Package required but not available: ‘ggplot2’

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

Package suggested but not available for checking: ‘CCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) lientz.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lientz.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lientz.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggbeeswarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'gamm4', 'gganimate', 'ggplot2', 'glmmTMB', 'lme4',
  'patchwork', 'rstanarm', 'see', '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?
  > #
  > # * 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’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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: 'testthat', 'ggplot2'

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

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', 'progress', 'purrr', 'tibble', 'tidypredict'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DALEX', 'auditor', 'ggplot2', 'kableExtra', 'archivist', 'devtools',
  'breakDown', 'drifter'

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

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

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

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

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

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’
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
checkRd: (-1) model.importance.plot.Rd:139: Lost braces
   139 | For binary CF models, if{importance.type = 2}, function uses AUC-based variables importances as described by Janitza et al. (2012). Here, the area under the curve instead of the accuracy is used to calculate the importance of each variable. This AUC-based variable importance measure is more robust towards class imbalance. 
       |                         ^
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', 'purrr', 'tibble', 'tidyr', '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:
  'DALEX', 'ingredients', 'iBreakDown', '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', 'brms', 'broom', 'broom.mixed', 'car', 'did', 'ggdist',
  'ggplot2', 'gh', 'gt', 'gtExtras', 'haven', 'huxtable', 'labelled',
  'IRdisplay', 'ivreg', 'kableExtra', 'lme4', 'magick', 'mice',
  'rstanarm', 'tibble', 'tidyselect', 'tidyverse', 'tinysnapshot'
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:
  'timetk', 'parsnip', 'dials', 'yardstick', 'workflows', 'hardhat',
  'plotly', 'gt', 'ggplot2', 'tibble', 'tidyr', 'dplyr', 'purrr',
  'stringr', 'forcats', 'janitor', 'forecast', 'prophet', 'tidyverse',
  'tidymodels'

Packages suggested but not available for checking:
  'rstan', 'slider', 'sparklyr', 'workflowsets', 'recipes', 'rsample',
  'tune', 'lubridate', 'progress', 'testthat', 'roxygen2', 'thief',
  'smooth', 'greybox', 'trelliscopejs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'modeltime', 'tune', 'rsample', 'workflows', 'parsnip', 'recipes',
  'dials', 'yardstick', 'timetk', 'tibble', 'dplyr', 'tidyr', 'purrr',
  'forcats', 'stringr', 'ggplot2', 'plotly', 'hardhat'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'tidymodels', 'tidyverse', 'tidyquant',
  'lubridate'

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: 'cowplot', 'ggplot2', 'reshape2'

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

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'openintro', 'patchwork', 'viridis', 'readr',
  'nycflights13'

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:
  > # 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 ‘metadata.Rmd’ using rmarkdown

Quitting from lines 12-14 [unnamed-chunk-1] (metadata.Rmd)
Error: processing vignette 'metadata.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘metadata.Rmd’

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

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

SUMMARY: processing the following file failed:
  ‘metadata.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.
Package required but not available: ‘markovchain’

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 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 suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Run all unit tests
  > 
  > testthat::test_check("MODISTools")
  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 ‘modistools-vignette.Rmd’ using knitr

Quitting from lines 13-30 [setup] (modistools-vignette.Rmd)
Error: processing vignette 'modistools-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘modistools-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'AER'
Running examples in ‘modmarg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: marg.ivreg
> ### Title: Predicted Margins for 'ivreg' objects from the 'AER' package
> ### Aliases: marg.ivreg
> 
> ### ** Examples
> 
> # From ?AER::ivreg
> 
> # data
> data("CigarettesSW", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Running ‘testthat.R’ [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’

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

Package suggested but not available for checking: ‘arm’

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:
  'purrr', 'stringr', 'MplusAutomation', 'dplyr', 'ggplot2'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: boot.mcor.ic
> ### Title: Intervalles de confiance bootstrap pour une matrice de
> ###   corrélation de Bravais-Pearson
> ### Aliases: boot.mcor.ic
> 
> ### ** Examples
> 
> data(Mesures5,package="BioStatR")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘BioStatR’
Calls: data -> find.package
Execution halted
Packages required but not available:
  'DescTools', 'C50', 'car', 'NeuralNetTools', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'devtools'
Packages suggested but not available for checking:
  'smoof', 'testthat', 'ggplot2', 'reshape2', 'pkgdown'
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: ‘clustMD’
Packages required but not available:
  'purrr', 'tibble', 'readr', 'stringr', 'dplyr', 'lubridate',
  '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: 'tidyr', 'stringr', 'compareDF'

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

Package suggested but not available for checking: ‘rglwidget’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
Packages required but not available:
  'dplyr', 'purrr', 'stringr', 'tidyr', 'tibble', 'arrow'

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

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
Package required but not available: ‘dplyr’

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

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

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggmap', 'lubridate', 'dplyr', 'moveHMM',
  'car'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rvest', '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.
Packages suggested but not available for checking:
  'nycflights13', 'ggplot2'
Packages suggested but not available for checking:
  'testthat', '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
checkRd: (-1) TemplateList-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TemplateList-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TemplateList-class.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TemplateList-class.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TemplateList-class.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bindEvents.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bindEvents.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bindEvents.Rd:28: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'testthat', 'pkgdown'
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: ‘optimx’

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

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

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', 'stringr', 'tibble', 'tidyr'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) legacy.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:40: 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:
  > ## load dependencies
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
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 ‘MonteCarlo-Vignette.Rmd’ using rmarkdown

Quitting from lines 316-320 [unnamed-chunk-15] (MonteCarlo-Vignette.Rmd)
Error: processing vignette 'MonteCarlo-Vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘MonteCarlo-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘MonteCarlo-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'blastula', 'magick', 'purrr', 'readr', 'readxl', 'snakecase',
  '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', 'tidytext', 'ggwordcloud', 'stringr', 'RMariaDB',
  'RSQLite', 'usethis', 'RPostgres'

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: 'sjmisc', 'stringr'

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

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

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

Packages suggested but not available for checking:
  'descriptio', 'caret', 'dplyr'

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

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

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:
  'piecemaker', 'purrr', 'readr', 'stringr'

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

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

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:
  'concaveman', 'ggplot2', 'automap', 'alphahull'

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

Package suggested but not available for checking: ‘testthat’

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

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

--- re-building ‘morrow-plots-data-visualizations.Rmd’ using rmarkdown

Quitting from lines 21-24 [setup] (morrow-plots-data-visualizations.Rmd)
Error: processing vignette 'morrow-plots-data-visualizations.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘morrow-plots-data-visualizations.Rmd’

--- re-building ‘national-yield-comparison.Rmd’ using rmarkdown
--- finished re-building ‘national-yield-comparison.Rmd’

--- re-building ‘plots-etcetera.Rmd’ using rmarkdown
--- finished re-building ‘plots-etcetera.Rmd’

SUMMARY: processing the following file failed:
  ‘morrow-plots-data-visualizations.Rmd’

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

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

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: 'tidyr', 'rvest'

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: 'tidyverse', 'reshape2'

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

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', 'plotly', 'testthat'

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

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

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

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

Package suggested but not available for checking: ‘mosaic’

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

Packages suggested but not available for checking:
  'ggstance', 'ggridges', 'vdiffr', 'lubridate', 'testthat', 'ggrepel',
  'readr', 'ggdendro', 'broom'

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.
Packages suggested but not available for checking:
  'annotate', 'bigstatsr', 'scatterpie', 'ggplot2', 'ggpmisc',
  'ggthemes', 'testthat', 'viridis'
checkRd: (-1) ssvdEN_sol_path.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol,
       |                                                     ^
checkRd: (-1) ssvdEN_sol_path_par.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{tol}{Convergence is determined when ||U_j - U_{j-1}||_F < tol,
       |                                                     ^
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 ‘MOSS_working_example.Rmd’ using rmarkdown

Quitting from lines 134-144 [unnamed-chunk-4] (MOSS_working_example.Rmd)
Error: processing vignette 'MOSS_working_example.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘MOSS_working_example.Rmd’

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

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

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

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: ‘tibble’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggraph', 'igraph', 'intergraph', 'network',
  'purrr', 'reshape2', 'tibble', 'tidygraph'

Packages suggested but not available for checking:
  'ergm', 'pkgdown', '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’
Running ‘testthat.R’ [0s/1s]
Running 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', '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 ‘mousetRajectory.Rmd’ using rmarkdown

Quitting from lines 73-76 [setup] (mousetRajectory.Rmd)
Error: processing vignette 'mousetRajectory.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘mousetRajectory.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', '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:
  'tidyselect', 'dplyr', 'tibble', 'vroom', 'vctrs'

Packages suggested but not available for checking:
  'purrr', 'ggplot2', 'testthat', 'lubridate', 'tidyr', 'gganimate',
  'ggspatial'

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

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

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

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', 'hms', 'igraph', 'osfr', '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:
  'ggmap', 'testthat', 'ggplot2', 'lubridate', 'amt', 'solartime'
checkRd: (-1) brownian.motion.variance.dyn.Rd:39: Lost braces
    39 |         \link{brownian.bridge.dyn}, link{dynBGBvariance}
       |                                         ^
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 ‘browseMovebank.Rmd’ using rmarkdown
--- finished re-building ‘browseMovebank.Rmd’

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

Quitting from lines 309-314 [unnamed-chunk-34] (move.Rmd)
Error: processing vignette 'move.Rmd' failed with diagnostics:
there is no package called 'lubridate'
--- failed re-building ‘move.Rmd’

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

Error: Vignette re-building failed.
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: 'rms', 'animation'

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

Packages suggested but not available for checking:
  'car', 'NeuralNetTools', 'pdp', 'vivid', 'AppliedPredictiveModeling'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) thresh.est.Rd:16: Lost braces
    16 |   Calculates the stimulus level(s) for a probit model of a psychometric function for given levels of performance.  For a more general version, see \link[MASS]{dose.p} in pkg{MASS}.
       |                                                                                                                                                                              ^
Packages required but not available: 'car', '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', 'tidyr', 'stringr', 'purrr', 'tibble'

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

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

Package suggested but not available for checking: ‘kableExtra’

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:
  'ggplot2', 'reshape2', 'dplyr', 'tidyr'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) apc.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) apc.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) apc.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) apc.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:31-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:36-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mpn.Rd:45: 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 required but not available: 'stringr', 'ggplot2', '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', 'ggplot2', 'purrr', 'reshape2', 'tibble', 'tidyr',
  'tidyselect'

Packages suggested but not available for checking:
  'bkmr', 'bws', 'infinitefactor', 'qgcomp', 'rstan', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', '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
checkRd: (-1) get.mpt.fia.Rd:60: Lost braces
    60 | \item{lnconst}{When inequality constraints are present, \code{lnconst} serves as an adjustment of code{lnInt}. It estimates the logarithm of the proportion of parameter space [0,1]^S that satisfies those inequality constraints, and the log integral term is given by \code{lnInt+lnconst}.
       |                                                                                                       ^
checkRd: (-1) prediction.plot.Rd:38: Lost braces
    38 | The labels on the x-axis. Default is \code{Tree 1} to code{Tree n}.
       |                                                           ^
Packages required but not available:
  'tidyr', 'dplyr', 'tibble', 'reshape2', '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:
  'dplyr', 'flowTraceR', 'forcats', 'ggplot2', 'plotly', 'purrr',
  'stringr', 'tibble', 'tidyr', 'UpSetR'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) F.huggins.estim.Rd:199: Escaped LaTeX specials: \$ \$
checkRd: (-1) F.huggins.estim.Rd:205: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:206: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:207: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:208: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:209: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:210: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:212: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:213: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:214: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:215: Escaped LaTeX specials: \$
checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
Package required but not available: ‘rstan’

Packages suggested but not available for checking:
  'testthat', 'tidyverse', 'ggplot2', 'ggmcmc', 'DescTools',
  'kableExtra', 'roxygen2', 'MendelianRandomization'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘keras’
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', 'fdapace', 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 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', '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:
  'purrr', 'ggplot2', 'dplyr', 'caret', 'reshape2', '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: 'ggplot2', 'reshape2'

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

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

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

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

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

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

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.
checkRd: (-1) MultiManhattan.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
checkRd: (-1) MultiManhattan.Rd:35: Lost braces; missing escapes or markup?
    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^
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:
  'GGally', 'Hmisc', 'mice', 'network', 'pcalg', 'sna', 'WGCNA'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bmi.bmi.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.bmi.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.bmi.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.sbp.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.sbp.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.sbp.Rd:16: Lost braces in \enumerate; meant \describe ?
Packages required but not available: 'caret', 'igraph'

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

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

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: 'plotly', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) msa-package.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa-package.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa-package.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:67: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.msa.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) n.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
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’

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 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: ‘cellranger’

Package suggested but not available for checking: ‘doconv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cp4p', 'caret', 'mixOmics', 'reshape2', 'ggplot2', 'dplyr',
  'fuzzyjoin', 'performanceEstimation', 'UBL', 'car'

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

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

Packages suggested but not available for checking: 'Synth', '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
Packages required but not available: 'phangorn', 'igraph'

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: 'testthat', 'rvest'
Running ‘testthat.R’ [0s/1s]
Running 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', 'mscstexta4r'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # testthat testing instructions are at http://r-pkgs.had.co.nz/tests.html
  > # quick notes:
  > #   put all your tests in tests/testthat folder
  > #   each test file should start with test and end in .R
  > #   since we use secret API keys, don't run the tests on CRAN
  > 
  > 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
Packages required but not available: 'ggplot2', 'lubridate'

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

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', 'ggrepel'

Packages suggested but not available for checking:
  'broom', 'kableExtra', 'r4ss', 'readxl', 'reshape2', 'rfishbase',
  'testthat', 'tidyr', 'usethis'

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

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
Found the following files/directories:
  ‘test.txt’
Packages suggested but not available for checking:
  'animation', 'igraph', 'ggplot2', 'sna'
Running examples in ‘MSG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: canabalt
> ### Title: The scores of the game Canabalt from Twitter
> ### Aliases: canabalt
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
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.
Packages required but not available:
  'purrr', 'dplyr', 'forcats', 'stringr', 'ggplot2', 'ggbeeswarm',
  'tidyr', 'tidyselect'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'babelgene', 'dplyr', 'tibble', '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:
  'do', 'rvest', 'set', 'kableExtra', 'dplyr', 'stringr', 'sqldf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ICAMS', '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:
  'dplyr', 'tibble', 'tidyr', 'caret', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'httr2', 'purrr', 'readr', 'tibble', 'tidyjson', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Packages required but not available:
  'BayesMallows', 'bmixture', 'dplyr', 'factoextra', 'ggbump',
  'ggplot2', 'spsUtil', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'flexsurv'
Running ‘test_base.R’ [0s/0s]
Running the tests in ‘tests/test_base.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following HTML validation problems:
tnorm.html:113:32 (tnorm.Rd:74): Warning: trimming empty <code>
Packages required but not available: 'ggplot2', 'patchwork'

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

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', 'ggpubr'

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

Package suggested but not available for checking: ‘tidyverse’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Cuminc
> ### Title: Plot method for Cuminc objects
> ### Aliases: plot.Cuminc
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘visuals_demo.Rmd’ using rmarkdown

Quitting from lines 30-36 [unnamed-chunk-2] (visuals_demo.Rmd)
Error: processing vignette 'visuals_demo.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘visuals_demo.Rmd’

--- re-building ‘Tutorial.Rnw’ using Sweave
Loading required package: survival
--- finished re-building ‘Tutorial.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘Rsctest.R’ [3s/5s]
  Running ‘testthat.R’ [0s/1s]
Running 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: ‘latex2exp’

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: '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: ‘igraph’

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

Packages suggested but not available for checking: 'httptest', '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: ‘testthat’
checkRd: (-1) multivar_joint_shannon_entropy.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
checkRd: (-1) total_correlation.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
'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.
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', '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: 'car', 'ggplot2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'car'
'LazyData' is specified without a 'data' directory
Running examples in ‘mthapower-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mthapower
> ### Title: Power calculations - mtDNA haplogroups
> ### Aliases: mthapower
> 
> ### ** Examples
> 
> # Example 1:
> pow <- mthapower(n.cases=203, p0=0.443, Nh=13, OR.cas.ctrl=2.33, sig.level=0.05)
> 
> # Example 2:
> # Create data frames
> pow.H150 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.5, sig.level=0.05)
> pow.H175 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.75, sig.level=0.05)
> pow.H200 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2, sig.level=0.05)
> pow.H250 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2.5, sig.level=0.05)
> 
> # Bind the three data frames:
> bindata <- rbind(pow.H150,pow.H175,pow.H200,pow.H250)
> # Adds column OR to binded data frame:
> bindata$OR <- rep(factor(c(1.50,1.75,2,2.5)),
+               times = c(nrow(pow.H150),
+                         nrow(pow.H175),
+                         nrow(pow.H200),
+                         nrow(pow.H250)))
> # Create plot:
> # install.packages("car")
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'reshape2', 'testthat', 'vdiffr'
'LazyData' is specified without a 'data' directory
Running examples in ‘MTLR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotcurves
> ### Title: Graphically Visualize MTLR Survival Curves
> ### Aliases: plotcurves
> 
> ### ** Examples
> 
> #Set up the example:
> library(survival)
> mod <- mtlr(Surv(time,status)~., data = lung)
> curves <- predict(mod, type = "survivalcurve")
> 
> plotcurves(curves, 1:10)
Error: Package "ggplot2" and "reshape2" are needed for this function to work. Please install them.
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 ‘workflow.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MTLR.Rcheck/vign_test/MTLR/vignettes/workflow_files/figure-html/unnamed-chunk-8-1.png
672x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5274 bytes
Input file size = 6132 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4661
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 4621
  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 = 4621

Output IDAT size = 4621 bytes (653 bytes decrease)
Output file size = 4699 bytes (1433 bytes = 23.37% decrease)


Quitting from lines 136-137 [unnamed-chunk-10] (workflow.Rmd)
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
Package "ggplot2" and "reshape2" are needed for this function to work. Please install them.
--- failed re-building ‘workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'ggplot2', 'reshape2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Guide.Rmd’ using rmarkdown

Quitting from lines 174-188 [unnamed-chunk-2] (Guide.Rmd)
Error: processing vignette 'Guide.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Guide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'magick', 'imager', 'dplR', 'measuRing', 'dplyr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggplot2', 'janitor', 'stringr', 'testthat',
  'tibble', '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 ‘mtsta_redlist.Rmd’ using rmarkdown

Quitting from lines 24-39 [unnamed-chunk-2] (mtsta_redlist.Rmd)
Error: processing vignette 'mtsta_redlist.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘mtsta_redlist.Rmd’

SUMMARY: processing the following file failed:
  ‘mtsta_redlist.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: '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: 'ggplot2', 'dplyr'

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

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

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

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

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

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

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: 'igraph', 'randomcoloR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘multbxxc/libs/multbxxc.so’:
  Found non-API calls to R: ‘IS_GROWABLE’, ‘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:
  'lme4', 'tram', 'glmmTMB'
Error(s) in re-building vignettes:
  ...
--- re-building ‘chfls1.Rnw’ using Sweave
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data

Attaching package: ‘TH.data’

The following object is masked from ‘package:MASS’:

    geyser

Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
--- finished re-building ‘chfls1.Rnw’

--- re-building ‘generalsiminf.Rnw’ using Sweave
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

The following object is masked from ‘package:MASS’:

    geyser


Attaching package: ‘robustbase’

The following object is masked from ‘package:survival’:

    heart


Error: processing vignette 'generalsiminf.Rnw' failed with diagnostics:
 chunk 2 (label = setup-2) 
Error in library("lme4") : there is no package called ‘lme4’

--- failed re-building ‘generalsiminf.Rnw’

--- re-building ‘multcomp-examples.Rnw’ using Sweave
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

The following object is masked from ‘package:MASS’:

    geyser

Waiting for profiling to be done...
Warning in chkdots(...) :
  Argument(s) ‘abseps’ passed to ‘...’ are ignored
--- finished re-building ‘multcomp-examples.Rnw’

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

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) MultEq-package.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:30: Lost braces in \itemize; meant \describe ?
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
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggstatsplot', 'ggplot2', 'dplyr', 'tibble', 'BayesFactor', 'broom',
  'car', 'highcharter', 'purrr', 'stringr'

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

Packages suggested but not available for checking:
  'readxl', 'readr', 'cowplot', 'reshape2', 'sjmisc', 'stringr',
  'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
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 ‘SIR-MCMC.Rmd’ using rmarkdown

Quitting from lines 121-130 [plot] (SIR-MCMC.Rmd)
Error: processing vignette 'SIR-MCMC.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘SIR-MCMC.Rmd’

--- re-building ‘SIRtrans.Rnw’ using knitr
--- finished re-building ‘SIRtrans.Rnw’

SUMMARY: processing the following file failed:
  ‘SIR-MCMC.Rmd’

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

Packages suggested but not available for checking:
  'phacking', 'PublicationBias', '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:
  'car', 'lme4', 'mixlm', 'plsVarSel', 'progress', 'SSBtools'

Packages suggested but not available for checking: 'FactoMineR', 'RGCCA'

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

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

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: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) dbivCMP.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
Packages required but not available: 'ggplot2', 'lme4'

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

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

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

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

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

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.
Packages required but not available:
  'dplyr', 'purrr', 'ez', 'stringr', 'reshape2', 'tibble', 'ggplot2',
  'BayesFactor', 'broom'

Packages suggested but not available for checking:
  'fastDummies', 'vctrs', 'tidyselect', 'tidyr', 'ggraph', 'testthat',
  'cowplot'

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

Packages suggested but not available for checking:
  'ggplot2', 'forcats', 'tidyr', 'patchwork', '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:
  > 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 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', 'cowplot', 'plsgenomics', 'ggrepel', 'qgraph', 'mgm',
  'lemon'

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:
  'brms', 'ggplot2', 'shinystan', 'plotly', 'hrbrthemes', 'loo',
  'bayesplot'

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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:
  'lme4', 'lmerTest', 'JWileymisc', 'cowplot', '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', 'klaR'

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: 'igraph', 'RecordLinkage', 'stringr'

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:
  'dplyr', 'lubridate', 'stringr', 'tidyselect', 'tidyr', 'sqldf'

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:
  'sand', 'statnet', 'testthat'

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

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'loo', 'tidygraph', 'pkgdown', 'flexsurv'

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
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:
  'cobalt', 'dplyr', 'optmatch', 'matchMulti'

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

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', 'magick'

Package suggested but not available for checking: ‘roxygen2’

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

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: 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'ggplot2', 'invGauss', 'pec', 'randomForestSRC', 'survminer', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'patchwork', '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.
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) nullestimation.Rd:17: Lost braces; missing escapes or markup?
    17 |           \code{U}        \tab The common latent space vectors. U in R^{n x d}\cr
       |                                                                        ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dplyr', 'ggplot2'
Package required but not available: ‘lme4’

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

Packages suggested but not available for checking:
  'tmap', 'cowplot', 'magick'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'igraph', '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:
  'DiagrammeR', 'dplyr', 'furrr', 'ggdist', 'ggplot2', 'purrr',
  'stringr', 'tibble', 'tidyr', 'lme4'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘CCA’
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:
  'factoextra', 'candisc', 'ggdendro', 'plotly', 'ecodist', 'ggplot2'

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', 'reshape2'

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

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'broom', 'gganimate', 'forcats', 'stringr',
  'cowplot', 'tidybayes', 'modelr', 'styler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
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:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'lme4', 'gamm4', 'geepack'

Packages which this enhances but not available for checking:
  'cplm', 'logistf', 'splm', 'unmarked'
Unknown package ‘wgeesel’ in Rd xrefs
checkRd: (-1) metricUnfolding.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:73-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:75-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:80-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLociHC.Rd:55: Lost braces; missing escapes or markup?
    55 | If \code{value} is one of {0.2,0.4,0.6,0.8,1,2,3,4,5,6,7,8,9,10}
       |                           ^
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running examples in ‘munsell-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chroma_slice
> ### Title: Plot all colours with the same chroma
> ### Aliases: chroma_slice
> 
> ### ** Examples
> 
> chroma_slice(2)
Error: ggplot2 needed for this function to work. Please install it.
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: ‘stringr’

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', '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: ‘lubridate’

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: ‘DescTools’
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: 'qvalue', 'testthat'
Running examples in ‘mutoss-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Qvalue
> ### Title: Storey's (2001) q-value Procedure...
> ### Aliases: Qvalue
> 
> ### ** Examples
> pval <- c(runif(50), runif(50, 0, 0.01))
> result <- Qvalue(pval)
Loading required package: qvalue
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘qvalue’
Package qvalue is required - should we install it?
Error in requireLibrary("qvalue") : 
  Required package qvalue should not be installed
Calls: Qvalue -> requireLibrary
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’

Packages suggested but not available for checking:
  'dplyr', 'reshape2', 'kableExtra'

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) cv.glm1path.Rd:74: Lost braces
    74 | \code{\link{glm1path}}, \\code{\link{glm1}}, \code{\link{glm}}, \code{\link{family}}
       |                               ^
Running ‘testthat.R’ [0s/1s]
Running 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: 'RLRsim', 'sem'
Packages required but not available: 'car', 'ggplot2', 'reshape2'

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

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

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:
  'brms', 'rstan', 'posterior', 'loo', 'bayesplot', 'ggplot2', 'purrr',
  'smooth', 'dplyr'

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

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘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: 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘mice’

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: 'Hmisc', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) dmvss.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/1s]
Running 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: ‘mpoly’

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:
  'dplyr', 'furrr', 'stringr', 'testthat', 'textmineR', 'tidytext'
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 ‘getting_started_with_mvrsquared.Rmd’ using rmarkdown

Quitting from lines 150-183 [unnamed-chunk-7] (getting_started_with_mvrsquared.Rmd)
Error: processing vignette 'getting_started_with_mvrsquared.Rmd' failed with diagnostics:
there is no package called 'tidytext'
--- failed re-building ‘getting_started_with_mvrsquared.Rmd’

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

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

Packages suggested but not available for checking:
  'PCMBaseCpp', 'ggplot2', 'mvMORPH', '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', 'ggsci'

Package suggested but not available for checking: ‘plotly’

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggplot2’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘mws-dependencies.Rmd’ using rmarkdown
--- finished re-building ‘mws-dependencies.Rmd’

--- re-building ‘mws-vignette.Rmd’ using rmarkdown

Quitting from lines 43-48 [load] (mws-vignette.Rmd)
Error: processing vignette 'mws-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘mws-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'nnTensor', 'ccTensor', 'iTensor', '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:
  'tidyr', 'purrr', 'dplyr', 'ggplot2', 'refund', 'reshape2',
  'SimDesign'

Packages suggested but not available for checking:
  'testthat', 'tidyverse', 'ggpubr', 'spatialTIME', 'tibble', 'broom',
  'refund.shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tidyverse'
Running ‘testthat.R’ [0s/1s]
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 ‘mmod_tutorial.Rmd’ due to unavailable dependencies:
  'tidyverse'
Packages required but not available: 'lme4', 'geepack', 'dplyr', 'Hmisc'

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

Packages suggested but not available for checking: 'janitor', '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 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:
  'stringr', 'lubridate', 'tibble', 'dplyr', 'purrr', 'tidyr',
  'ggplot2', 'ggforce', 'viridis', 'plotly', 'vroom', 'progress'

Packages suggested but not available for checking:
  'kableExtra', 'rTubeDB', '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’
Package required but not available: ‘car’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
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: 'rvest', 'tibble', 'httr2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(N2R)
  Loading required package: Matrix
  > 
  > testthat::test_check("N2R")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages suggested but not available for checking:
  'devtools', 'testthat', 'roxygen2', 'rvest'
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: 'ggplot2', 'ggforce', 'ggrepel'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SCORE
> ### Title: Spectral Clustering On Ratios-of-Eigenvectors.
> ### Aliases: SCORE
> 
> ### ** Examples
> 
> 
> # Simulate the Network
> n = 10; K = 2;
> theta = 0.4 + (0.45-0.05)*(seq(1:n)/n)^2; Theta = diag(theta);
> P  = matrix(c(0.8, 0.2, 0.2, 0.8), byrow = TRUE, nrow = K)
> set.seed(2022)
> l = sample(1:K, n, replace=TRUE); # node labels
> Pi = matrix(0, n, K) # label matrix
> for (k in 1:K){
+   Pi[l == k, k] = 1
+ }
> Omega = Theta %*% Pi %*% P %*% t(Pi) %*% Theta;
> Adj = matrix(runif(n*n, 0, 1), nrow = n);
> Adj = Omega - Adj;
> Adj = 1*(Adj >= 0)
> diag(Adj) = 0
> Adj[lower.tri(Adj)] = t(Adj)[lower.tri(Adj)]
> library(igraph)
Error in library(igraph) : there is no package called ‘igraph’
Execution halted
Packages required but not available: 'EnvStats', 'survminer'

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

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

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘asreml’
checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M36NT2PM.dat.Rd:38: Lost braces in \itemize; meant \describe ?
'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 suggested but not available for checking:
  'purrr', 'readxl', 'testthat', 'usethis'
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: 'igraph', 'ggraph', '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:
  'purrr', 'ggplot2', 'readr', 'lubridate', 'imputeTS', 'greybox',
  'fastDummies'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) DSIVdata.Rd:15-23: Lost braces
    15 | for(i in 1:50){
       |               ^
checkRd: (-1) DSIVdata.Rd:17-21: Lost braces
    17 |   for(j in 1:50){
       |                 ^
checkRd: (-1) DSIVdata.Rd:31-39: Lost braces
    31 | for(i in 1:20){
       |               ^
checkRd: (-1) DSIVdata.Rd:33-37: Lost braces
    33 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:10-18: Lost braces
    10 | for(i in 1:200){
       |                ^
checkRd: (-1) DSLIVEdata.Rd:12-16: Lost braces
    12 |   for(j in 1:200){
       |                  ^
checkRd: (-1) DSLIVEdata.Rd:26-34: Lost braces
    26 | for(i in 1:20){
       |               ^
checkRd: (-1) DSLIVEdata.Rd:28-32: Lost braces
    28 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:50-54: Lost braces
    50 | for(kk in 1:length(p)){
       |                       ^
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:
  'bib2df', 'dplyr', 'lubridate', 'readr', 'stringr'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: '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:
  'autothresholdr', 'detrendr', 'dplyr', 'filesstrings', 'ggplot2',
  'ijtiff', 'purrr', 'reshape2', 'stringr', 'viridis'

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', 'ggplot2', 'purrr', 'tidyr', 'tibble', 'visdat', 'forcats',
  'viridis', 'UpSetR', 'vctrs'

Packages suggested but not available for checking:
  'testthat', 'wakefield', 'vdiffr', 'simputation', 'imputeTS', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'blob', 'hms', 'testthat', 'tibble', 'vctrs'
Running examples in ‘nanoarrow-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: na_vctrs
> ### Title: Vctrs extension type
> ### Aliases: na_vctrs
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("jsonlite", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ vctr <- as.POSIXlt("2000-01-02 03:45", tz = "UTC")
+ array <- as_nanoarrow_array(vctr, schema = na_vctrs(vctr))
+ infer_nanoarrow_ptype(array)
+ convert_array(array)
+ ## Don't show: 
+ }) # examplesIf
> vctr <- as.POSIXlt("2000-01-02 03:45", tz = "UTC")
> array <- as_nanoarrow_array(vctr, schema = na_vctrs(vctr))
Error in loadNamespace(x) : there is no package called ‘vctrs’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Licensed to the Apache Software Foundation (ASF) under one
  > # or more contributor license agreements.  See the NOTICE file
  > # distributed with this work for additional information
  > # regarding copyright ownership.  The ASF licenses this file
  > # to you under the Apache License, Version 2.0 (the
  > # "License"); you may not use this file except in compliance
  > # with the License.  You may obtain a copy of the License at
  > #
  > #   http://www.apache.org/licenses/LICENSE-2.0
  > #
  > # Unless required by applicable law or agreed to in writing,
  > # software distributed under the License is distributed on an
  > # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
  > # KIND, either express or implied.  See the License for the
  > # specific language governing permissions and limitations
  > # under the License.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'arrow', 'hms', 'mockery', 'pillar', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > testthat::test_check("nanoparquet")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  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.
Specified C++11: please drop specification unless essential
checkRd: (-1) nanoperiod.Rd:268: Lost braces
   268 | possible to use the binary operator `code{+}`. Instead the
       |                                          ^
File ‘nanotime/libs/nanotime.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.
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: ‘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: ‘car’

Package suggested but not available for checking: ‘testthat’

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

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', 'tidyr'

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

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: 'lubridate', 'readr', 'tibble'

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

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
Package required but not available: ‘beepr’

Packages suggested but not available for checking:
  'spatialClust', '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:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'gh', 'usethis'

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

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

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’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'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: ‘ggplot2’

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: ‘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: 'caret', 'ggplot2'

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

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

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 ‘issue-1.R’ [0s/1s]
  Running ‘issue-2.R’ [0s/1s]
  Running ‘issue-3.R’ [0s/1s]
  Running ‘spec.R’ [0s/1s]
Running the tests in ‘tests/issue-1.R’ failed.
Complete output:
  > stopifnot(require(testthat))
  Loading required package: testthat
  Error: require(testthat) is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/issue-2.R’ failed.
Complete output:
  > stopifnot(require(testthat))
  Loading required package: testthat
  Error: require(testthat) is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/issue-3.R’ failed.
Complete output:
  > stopifnot(require(testthat))
  Loading required package: testthat
  Error: require(testthat) is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/spec.R’ failed.
Complete output:
  > stopifnot(require(testthat))
  Loading required package: testthat
  Error: require(testthat) is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'roxygen2'
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: 'plotly', 'simts'

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

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/1s]
Running the tests in ‘tests/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:
  'ggplot2', 'rvest', 'stringr'

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.
Package suggested but not available for checking: ‘testthat’

Package which this enhances but not available for checking: ‘openVA’
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                 ^
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                         ^
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) nbconvert.Rd:49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) nbconvert.Rd:50: Lost braces in \enumerate; meant \describe ?
Running ‘testthat.R’ [0s/1s]
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: ‘dplyr’
Package required but not available: ‘rrpack’

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: '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
Package required but not available: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
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.
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', 'lubridate', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'Hmisc', 'igraph', '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', 'dplyr', 'readr', 'PopED', 'purrr', 'tibble', '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: '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:
  'RBesT', 'ggplot2', 'lmerTest', 'spaMM', 'magick'

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’

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

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: ‘dplyr’

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', '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
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ncpen.Rd:108: Lost braces; missing escapes or markup?
   108 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
checkRd: (-1) ncpen.reg.Rd:109: Lost braces; missing escapes or markup?
   109 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr', 'reshape2', 'arrow'
'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:
  'car', 'dplyr', 'stringr', 'tidycensus', 'tidyr'

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

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: ‘Hmisc’

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

Packages suggested but not available for checking:
  'tergm', 'ergm', 'tsna', 'testthat'

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

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

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:
  'viridis', 'MBESS', 'car', 'ez', 'BayesFactor', 'ggplot2', 'ggpubr'

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

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

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: ‘roxygen2’
Packages required but not available:
  'DescTools', 'ez', 'ggplot2', 'dplyr', 'fungible', 'rockchalk',
  'MBESS'

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

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

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', 'lubridate', 'neonUtilities', 'tidyselect', 'caret',
  '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', 'neonUtilities'
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:
  'neonUtilities', 'ggplot2', 'dtplyr', 'dplyr', 'lubridate',
  'stringr', 'tibble', 'tidyr', 'ggpubr'

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

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

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

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

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

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

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

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

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: ‘dplyr’

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

Packages suggested but not available for checking:
  'ggbeeswarm', 'ggpubr', 'hsstan'

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

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

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

Packages suggested but not available for checking:
  'broom', 'ggrepel', 'hardhat', 'patchwork', 'roxygen2', 'testthat',
  'tidyselect', 'tune', 'vdiffr', 'workflows'

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/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.
Packages required but not available: 'vctrs', '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:
  'ggplot2', 'igraph', 'roxygen2', 'testthat'
Running examples in ‘net4pg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_cc
> ### Title: Plot peptide-to-protein mapping graph
> ### Aliases: plot_cc
> 
> ### ** Examples
> 
> library(igraph)
Error in library(igraph) : there is no package called ‘igraph’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_To_net4pg.Rmd’ using rmarkdown

Quitting from lines 99-102 [unnamed-chunk-1] (Intro_To_net4pg.Rmd)
Error: processing vignette 'Intro_To_net4pg.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘Intro_To_net4pg.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_To_net4pg.Rmd’

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

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.
Specified C++11: please drop specification unless essential
Package required but not available: ‘ggplot2’

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: 'rD3plot', 'igraph', 'haven'

Package suggested but not available for checking: ‘readr’

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

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:
  'dplyr', 'igraph', 'pcalg', 'purrr', 'tibble', 'tidyselect',
  'tidygraph'

Packages suggested but not available for checking:
  'broom', '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:
  > # 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:
  'sna', 'network', 'networkDynamic', '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', 'igraph', 'ggplot2', 'ggraph', 'patchwork', 'tibble',
  'tidygraph', '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:
  'AnnotationDbi', 'dplyr', 'genefilter', 'graphite', 'igraph',
  'msigdbr', 'org.Hs.eg.db', 'RCy3', 'reshape2'

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

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:
  'fastshp', 'SpaDES.core', '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:
  'ggnetwork', 'igraph', 'network', 'sna'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'btergm', 'ergm', 'sna', 'network', 'ergMargins', 'lme4',
  'intergraph'

Packages suggested but not available for checking:
  'igraph', 'relevent', 'statnet'

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

Package suggested but not available for checking: ‘igraph’

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

Packages suggested but not available for checking:
  'ergm', 'ggplot2', 'network'

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

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

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

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: ‘knitcitations’
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: 'ggraph', 'ggplot2', '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', 'fable', 'fabletools', 'igraph', 'tibble', 'tidyr',
  'tsibble'

Package suggested but not available for checking: ‘feasts’

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: ‘DiagrammeR’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', '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: ‘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:
  'testthat', 'igraph', 'ggplot2', 'dplyr', 'tidyr', 'tibble',
  'mixtools', 'EnvStats', 'purrr'
checkRd: (-1) spec_clust.Rd:33: Lost braces; missing escapes or markup?
    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
Running examples in ‘nett-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fast_cpl
> ### Title: CPL algorithm for community detection (fast)
> ### Aliases: fast_cpl
> ### Keywords: comm_detect
> 
> ### ** Examples
> 
> head(fast_cpl(igraph::as_adj(polblogs), 2), 50)
Error: Package "mixtools" needed for this function. Please install it.
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 ‘Community_Detection.Rmd’ using rmarkdown

Quitting from lines 24-35 [unnamed-chunk-2] (Community_Detection.Rmd)
Error: processing vignette 'Community_Detection.Rmd' failed with diagnostics:
there is no package called 'EnvStats'
--- failed re-building ‘Community_Detection.Rmd’

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

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

--- re-building ‘explore-comm.Rmd’ using rmarkdown

Quitting from lines 25-36 [unnamed-chunk-2] (explore-comm.Rmd)
Error: processing vignette 'explore-comm.Rmd' failed with diagnostics:
there is no package called 'EnvStats'
--- failed re-building ‘explore-comm.Rmd’

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

Quitting from lines 104-116 [unnamed-chunk-3] (hard_dcsbm_testing.Rmd)
Error: processing vignette 'hard_dcsbm_testing.Rmd' failed with diagnostics:
there is no package called 'EnvStats'
--- failed re-building ‘hard_dcsbm_testing.Rmd’

SUMMARY: processing the following files failed:
  ‘Community_Detection.Rmd’ ‘Visualization.Rmd’ ‘explore-comm.Rmd’
  ‘hard_dcsbm_testing.Rmd’

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

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.
checkRd: (-1) rc.plot.ideogram.Rd:20: Lost braces; missing escapes or markup?
    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
Packages required but not available: 'network', 'sna'

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', 'tidyr', 'igraph', 'qgraph', 'network', 'ggrepel',
  'GGally', 'ggvis'

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

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

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

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: 'igraph', 'network'

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

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

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', 'igraph', 'network', 'sna', 'tidyr',
  'purrr', 'patchwork'

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

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

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

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

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

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', 'igraph'

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 required but not available: ‘rstan’

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

Package suggested but not available for checking: ‘googledrive’

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

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

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

Package suggested but not available for checking: ‘fxregime’

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

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', 'NeuralNetTools', 'reshape2', 'caret', 'fastDummies',
  'stringr', 'Hmisc', 'ggforce', 'ggnewscale', 'ggrepel', 'ggbreak',
  'dplyr'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr', 'reshape2'
Running examples in ‘neurobase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: applyEmptyImageDimensions-methods
> ### Title: Apply Subsetting from Empty Image Dimensions
> ### Aliases: applyEmptyImageDimensions-methods applyEmptyImageDimensions
> ###   applyEmptyImageDimensions,nifti-method
> ###   applyEmptyImageDimensions,character-method
> ###   applyEmptyImageDimensions,factor-method
> ###   applyEmptyImageDimensions,list-method
> ###   applyEmptyImageDimensions,array-method
> ###   applyEmptyImageDimensions,anlz-method
> ###   applyEmptyImageDimensions,ANY-method apply_empty_dim
> 
> ### ** Examples
> 
> set.seed(5)
> dims = rep(10, 3)
> arr = array(rnorm(prod(dims)), dim = dims)
> arr[,,10] = 0
> nim = oro.nifti::nifti(arr)
> inds = getEmptyImageDimensions(nim)
> inds_arr = getEmptyImageDimensions(arr)
> testthat::expect_equal(inds, inds_arr)
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
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:
  'dplyr', 'forcats', 'ggplot2', '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: ‘dplyr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hcp.Rmd’ using rmarkdown

Quitting from lines 15-18 [setup] (hcp.Rmd)
Error: processing vignette 'hcp.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘hcp.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpmisc', 'cowplot'

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', 'tidyr', 'dplyr', 'purrr', 'tibble', 'forcats', 'ggplot2',
  'flipr', 'furrr', 'rgeomstats'

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:
  > # 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/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: 'devtools', 'tidyr', 'lubridate'

Packages suggested but not available for checking:
  'dplyr', 'robotstxt', 'rvest', 'stringr', 'testthat', 'mockery',
  'tidytext', 'textdata'

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

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:
  > 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("newsmap")
  Error in test_check("newsmap") : could not find function "test_check"
  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: ‘r2dictionary’
Packages suggested but not available for checking: 'igraph', 'tinysnapshot'
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
Packages required but not available:
  'dplyr', 'janitor', 'nflfastR', 'purrr', 'stringr', 'tibble',
  'tidyr', 'tidyselect'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'gh', 'piggyback', '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', 'purrr', 'tibble', 'tidyr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nfl4th', 'nflfastR', 'nflplotR', 'nflseedR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++14: please drop specification unless essential
Package required but not available: ‘fda’

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

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 which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'stringr', '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 required but not available: 'stringr', 'rvest'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mosaic’
checkRd: (-1) NHANES.Rd:278: Lost braces
   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
Packages required but not available:
  'hydroloom', 'dataRetrieval', 'dplyr', 'tidyr', 'maptiles', 'arrow'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
'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.
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', 'purrr', '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: ‘tibble’

Packages suggested but not available for checking:
  'dplyr', 'caret', 'readr', 'rsample', 'ggplot2', 'lme4', 'ggrepel',
  'lubridate', 'tidyr', 'forcats', 'janitor', 'synthpop'

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

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

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) bootstrap_param_est.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_data.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/1s]
Running 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 required but not available: 'dplyr', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'ggtext', 'ggh4x', 'janitor', 'patchwork', 'SIBER',
  'stringr', 'testthat'

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

Package suggested but not available for checking: ‘phytools’

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

Quitting from lines 20-25 [setup] (color-palette-demo.Rmd)
Error: processing vignette 'color-palette-demo.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘color-palette-demo.Rmd’

SUMMARY: processing the following file failed:
  ‘color-palette-demo.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', 'thematic', '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:
  'plotly', 'tidyr', 'bipartite', 'dplyr', 'ggplot2', 'igraph',
  'purrr', 'skimr', 'bnstruct', 'mice', 'missMDA', 'networkD3',
  'tibble', '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', 'ggthemes', 'dplyr'

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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', 'mcmcse'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: 'testthat', 'kableExtra'
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: ‘tibble’

Packages which this enhances but not available for checking:
  'kokudosuuchi', 'estatapi', 'jpndistrict', 'jpmesh'

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.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘car’

Packages suggested but not available for checking:
  'reshape2', 'ggplot2', 'rsq'

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

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', 'httr2', 'lubridate', 'tidyr', 'tidyselect',
  'tsibble'

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'lubridate', 'readr', 'dplyr', 'stringr', 'tidyselect'

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

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

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.
Specified C++11: please drop specification unless essential
Packages required but not available: 'purrr', 'term', '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', 'sqldf', 'ggplot2', 'saemix', 'sitar', 'fastDummies'

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 ‘Pwr1.R’ [0s/1s]
  Running ‘Pwr2.R’ [0s/1s]
  Running ‘logLik1.R’ [1s/1s]
  Running ‘missPat.R’ [0s/1s]
  Running ‘roxygen.R’ [0s/1s]
  Running ‘runScript.R’ [0s/1s]
  Running ‘simY.R’ [1s/2s]
Running the tests in ‘tests/Pwr1.R’ failed.
Complete output:
  > date()
  [1] "Wed Jun 12 16:09:46 2024"
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/missPat.R’ failed.
Complete output:
  > library(nlmeU)
  
  Attaching package: 'nlmeU'
  
  The following object is masked from 'package:stats':
  
      sigma
  
  > dtf <- subset(armd.wide, select = c(visual12, visual24, visual52))
  > res <-  missPat(dtf, symbols = c("?","+"))
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/roxygen.R’ failed.
Complete output:
  > library(roxygen2)
  Error in library(roxygen2) : there is no package called 'roxygen2'
  Execution halted
Packages required but not available: 'Hmisc', 'optimx', 'ggplot2'

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

Packages suggested but not available for checking:
  'broom.mixed', 'devtools', 'dplyr', 'nloptr', 'testthat', 'tibble',
  'xgxr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggtext', 'nlmixr2est', 'rxode2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nlmixr2est', 'rxode2'

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', 'nlmixr2est', 'nlmixr2extra', 'rxode2', 'vpc', 'xgxr'

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:
  'nlmixr2est', 'nlmixr2extra', 'rxode2', 'nlmixr2plot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggforce', 'ggpubr', 'ggplot2', 'stringr', 'nlmixr2',
  'nlmixr2extra', 'onbrand', 'rxode2', 'xpose', 'xpose.nlmixr2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'optimx', 'Rvmmin', 'Rcgmin'
Error(s) in re-building vignettes:
  ...
--- re-building ‘nlmrt-vignette.Rnw’ using Sweave
Loading required package: nlmrt
Error in nlsModel(formula, mf, start, wts, scaleOffset = scOff, nDcentral = nDcntr) : 
  singular gradient matrix at initial parameter estimates
Error in nls(regmod, start = huetstart, trace = FALSE, data = pastured) : 
  singular gradient
Loading required package: optimx
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘optimx’

Error: processing vignette 'nlmrt-vignette.Rnw' failed with diagnostics:
 chunk 10 (label = chunk10) 
Error in optimx(st, shobbs.f, shobbs.g, control = list(all.methods = TRUE)) : 
  could not find function "optimx"

--- failed re-building ‘nlmrt-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘nlmrt-vignette.Rnw’

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

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: ‘testthat’

Package suggested but not available for checking: ‘testthat’

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

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', 'stringr', 'readr'

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

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

Quitting from lines 21-25 [setup2] (Bootstrapping.Rmd)
Error: processing vignette 'Bootstrapping.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Bootstrapping.Rmd’

--- re-building ‘Confidence-Bands.Rmd’ using rmarkdown

Quitting from lines 21-25 [setup2] (Confidence-Bands.Rmd)
Error: processing vignette 'Confidence-Bands.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Confidence-Bands.Rmd’

--- re-building ‘Models-and-Functions.Rmd’ using rmarkdown

Quitting from lines 15-20 [setup] (Models-and-Functions.Rmd)
Error: processing vignette 'Models-and-Functions.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Models-and-Functions.Rmd’

--- re-building ‘nlraa-AgronJ-paper.Rmd’ using rmarkdown

Quitting from lines 15-20 [setup] (nlraa-AgronJ-paper.Rmd)
Error: processing vignette 'nlraa-AgronJ-paper.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘nlraa-AgronJ-paper.Rmd’

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

Quitting from lines 15-18 [setup] (nlraa.Rmd)
Error: processing vignette 'nlraa.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘nlraa.Rmd’

SUMMARY: processing the following files failed:
  ‘Bootstrapping.Rmd’ ‘Confidence-Bands.Rmd’ ‘Models-and-Functions.Rmd’
  ‘nlraa-AgronJ-paper.Rmd’ ‘nlraa.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Packages required but not available: 'rms', 'Hmisc'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) anova.Rd:19: Lost braces
    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
Package required but not available: ‘nloptr’

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

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

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

Quitting from lines 156-196 [opx] (FixedParameters.Rmd)
Error: processing vignette 'FixedParameters.Rmd' failed with diagnostics:
could not find function "Rvmmin"
--- failed re-building ‘FixedParameters.Rmd’

--- re-building ‘Intro-to-nlsr.Rmd’ using rmarkdown
--- finished re-building ‘Intro-to-nlsr.Rmd’

--- re-building ‘R-analytic-derivatives.Rmd’ using rmarkdown
Loading required package: Ryacas

Attaching package: 'Ryacas'

The following object is masked from 'package:stats':

    integrate

The following objects are masked from 'package:base':

    %*%, det, diag, diag<-, lower.tri, upper.tri

--- finished re-building ‘R-analytic-derivatives.Rmd’

--- re-building ‘nlsr-derivs.Rmd’ using rmarkdown
Loading required package: Ryacas

Attaching package: 'Ryacas'

The following object is masked from 'package:stats':

    integrate

The following objects are masked from 'package:base':

    %*%, det, diag, diag<-, lower.tri, upper.tri

--- finished re-building ‘nlsr-derivs.Rmd’

--- re-building ‘nlsr-devdoc.Rmd’ using rmarkdown

Quitting from lines 1600-1620 [maskRvmmin] (nlsr-devdoc.Rmd)
Error: processing vignette 'nlsr-devdoc.Rmd' failed with diagnostics:
could not find function "Rvmmin"
--- failed re-building ‘nlsr-devdoc.Rmd’

SUMMARY: processing the following files failed:
  ‘FixedParameters.Rmd’ ‘nlsr-devdoc.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.
Packages suggested but not available for checking:
  'devtools', 'dplyr', 'ggplot2', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...3,9c3,6
< > if (requireNamespace("spelling", quietly = TRUE)) {
< +   spelling::spell_check_test(
< +     vignettes = TRUE, error = FALSE,
< +     skip_on_cran = TRUE
< +   )
< + }
< NULL
---
> > if(requireNamespace('spelling', quietly = TRUE))
> +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
> +                              skip_on_cran = TRUE)
> 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘about.Rmd’ using rmarkdown
--- finished re-building ‘about.Rmd’

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

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

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

--- re-building ‘nls-investigator.Rmd’ using rmarkdown
--- finished re-building ‘nls-investigator.Rmd’

--- re-building ‘nlsy-ace.Rmd’ using rmarkdown

Quitting from lines 469-471 [session-info-2] (nlsy-ace.Rmd)
Error: processing vignette 'nlsy-ace.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘nlsy-ace.Rmd’

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

--- re-building ‘software-and-support.Rmd’ using rmarkdown
--- finished re-building ‘software-and-support.Rmd’

SUMMARY: processing the following file failed:
  ‘nlsy-ace.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) fwtnpperm.Rd:34: Lost braces
    34 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
Packages suggested but not available for checking:
  'TreeSim', 'DDD', 'ggplot2', 'Hmisc', 'reshape2', 'testthat',
  'DAISIE'
checkRd: (-1) check_input_event_times.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_input_event_times.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_time_unit.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_time_unit.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_params_doc.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_params_doc.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:39-40: 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 required but not available: 'devtools', 'readxl'

Package suggested but not available for checking: ‘netmeta’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'INLA', '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:
  'netmeta', 'meta', 'reshape2', '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:
  'meta', 'netmeta', '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: 'ggplot2', '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.
Package suggested but not available for checking: ‘ggplot2’
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tibble'
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
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: 'stringr', 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘devtools’

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

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

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

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: ‘readxl’
Package suggested but not available for checking: ‘ggpubr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMRphasing_vignette.rmd’ using rmarkdown

Quitting from lines 57-70 [unnamed-chunk-4] (NMRphasing_vignette.rmd)
Error: processing vignette 'NMRphasing_vignette.rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building ‘NMRphasing_vignette.rmd’

SUMMARY: processing the following file failed:
  ‘NMRphasing_vignette.rmd’

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

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', 'ggplot2', 'patchwork', 'tracee', 'tidyvpc'
Running ‘testthat.R’ [0s/1s]
Running 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', 'ggplot2', 'tidyr', 'forcats'

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:
  'keras', 'tensorflow', 'luz', 'cowplot', 'ggplot2', 'patchwork',
  'testthat', 'vdiffr'
Specified C++14: please drop specification unless essential
Running examples in ‘nn2poly-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.nn2poly
> ### Title: Plot method for 'nn2poly' objects.
> ### Aliases: plot.nn2poly
> 
> ### ** Examples
> 
> # --- Single polynomial output ---
> # Build a NN structure with random weights, with 2 (+ bias) inputs,
> # 4 (+bias) neurons in the first hidden layer with "tanh" activation
> # function, 4 (+bias) neurons in the second hidden layer with "softplus",
> # and 2 "linear" output units
> 
> weights_layer_1 <- matrix(rnorm(12), nrow = 3, ncol = 4)
> weights_layer_2 <- matrix(rnorm(20), nrow = 5, ncol = 4)
> weights_layer_3 <- matrix(rnorm(5), nrow = 5, ncol = 1)
> 
> # Set it as a list with activation functions as names
> nn_object = list("tanh" = weights_layer_1,
+                  "softplus" = weights_layer_2,
+                  "linear" = weights_layer_3)
> 
> # Obtain the polynomial representation (order = 3) of that neural network
> final_poly <- nn2poly(nn_object, max_order = 3)
> 
> # Plot all the coefficients, one plot per output unit
> plot(final_poly)
Error: package 'ggplot2' is required for this functionality
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
Found the following HTML validation problems:
nn2poly.html:129:1 (nn2poly.Rd:75): Warning: trimming empty <li>
nn2poly.html:128:1 (nn2poly.Rd:75): Warning: trimming empty <ol>
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'furrr', 'tidyr', 'igraph', 'ggplot2'

Packages suggested but not available for checking:
  'future.batchtools', 'logistf', 'mice'

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: 'forecast', 'tsutils'

Package suggested but not available for checking: ‘thief’

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

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: ‘stringr’

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’

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'dplyr', 'dbplyr', 'testthat', 'tibble', 'vroom'
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:114-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:121-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:125: Lost braces in \itemize; meant \describe ?
Running examples in ‘noctua-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: noctua_options
> ### Title: A method to configure noctua backend options.
> ### Aliases: noctua_options
> 
> ### ** Examples
> 
> library(noctua)
> 
> # change file parser from default data.table to vroom
> noctua_options("vroom")
Error: Please install vroom package 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 suggested but not available for checking:
  'RSQLite', 'RPostgres', '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
Error(s) in re-building vignettes:
  ...
--- re-building ‘nodbi-overview.Rmd’ using rmarkdown

Quitting from lines 45-66 [unnamed-chunk-2] (nodbi-overview.Rmd)
Error: processing vignette 'nodbi-overview.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 ‘nodbi-overview.Rmd’

SUMMARY: processing the following file failed:
  ‘nodbi-overview.Rmd’

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

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

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

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', '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
checkRd: (-1) simulatePop.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:45: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'caret', 'ggplot2', 'ExtDist', 'stringr', 'C50'

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: 'tibble', 'dplyr', '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: 'igraph', 'huge'

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: ‘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:
  'arcgeocoder', 'ggplot2', 'testthat', 'tibble', 'tidygeocoder'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
  'caret', 'dplyr', 'ggplot2', 'tidyverse', 'purrr'

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

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

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: 'rxode2', 'ggplot2', 'ggforce'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'nonmemica', 'nonmem2R', 'dplyr', 'xgxr',
  'vdiffr'

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

Package suggested but not available for checking: ‘wrangle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tidySEM', 'AER', 'faraway', 'mlogit', '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: ‘Hmisc’

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

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.
Package required but not available: ‘mlogit’

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: ‘dplyr’

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: 'dplyr', 'ggplot2', 'rio', '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: ‘purrr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mle_parameters.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'doBy', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'tibble', 'dplyr', 'emojifont', 'rio', 'ggplot2',
  'ggthemes', 'badger', '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 ‘clr1-tst.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: 'forecast', 'ggplot2', 'cowplot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'igraph', 'ggplot2', 'ggnetwork', 'intergraph',
  'viridis', 'gganimate', 'tidytree', 'treeio', 'ggtree', 'dplyr'
Package unavailable to check Rd xrefs: ‘treeio’
Note: skipping ‘continuous.Rmd’ due to unavailable dependencies: 'ggplot2'
Note: skipping ‘discrete.Rmd’ due to unavailable dependencies: 'ggplot2'
Note: skipping ‘none.Rmd’ due to unavailable dependencies: 'ggplot2'
Note: skipping ‘nosoi.Rmd’ due to unavailable dependencies: 'ggplot2'
Packages required but not available: 'dplyr', 'bipartite'

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: 'brms', '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: 'readxl', 'ggplot2', 'ggpattern'

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

Package suggested but not available for checking: ‘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', 'stringr'

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', 'dplyr', 'bayesplot'

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

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', 'MKinfer'

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) plot.regression.circular.Rd:35: Lost braces
    35 |               code{plot.type="circle"} and \code{x} is the output of \code{\link{kern.reg.circ.lin}}) or to \code{\link{lines3d}} (if \code{plot.type="circle"})
       |                   ^
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:
  'smotefamily', 'caret', 'dplyr', 'forcats', 'ggplot2', 'tidyr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) DiscHazRateAuxFunctions.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:48: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘styler’

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

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

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

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

Packages suggested but not available for checking:
  'httptest', 'mockery', '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.
checkRd: (-1) nplr.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:52-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:56-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:82: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'dplyr', 'tidyr', 'purrr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Package required but not available: ‘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: ‘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 ‘testthat.R’ [0s/1s]
Running 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:
  'profileR', 'car', 'dplyr'
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'tibble', 'ggplot2'
checkRd: (-1) np.reg.test.Rd:148: Lost braces
   148 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
checkRd: (-1) nptest-package.Rd:73: Lost braces
    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
Packages required but not available: 'broom', 'dplyr', 'srvyr', 'tidyr'

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

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/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
checkRd: (-1) NSAE.Rd:14: Lost braces; missing escapes or markup?
    14 | {Maintainer}: Saurav Guha \email{saurav.iasri@gmail.com}
       | ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'CCA', 'roxygen2', 'testthat'
checkRd: (-1) NScluster-package.Rd:30-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:35-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:44-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:49-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:44-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:69-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:113-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:36-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:90-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:123-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:151-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:195-211: Lost braces in \itemize; meant \describe ?
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:
  > # 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: ‘mcmcse’

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', 'rvest', 'stringr', 'dplyr', 'lubridate', 'purrr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'stringr'
File ‘nseval/libs/nseval.so’:
  Found non-API calls to R: ‘R_PromiseExpr’, ‘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
Packages required but not available: 'mlr', 'rPref'

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: ‘NSM3’
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Package required but not available: ‘sde’

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

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

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

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:
  'dplyr', 'lubridate', 'purrr', 'readxl', 'rvest', 'tidyr'

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', '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) MSM.fit.Rd:21: Lost braces
    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
checkRd: (-1) SMC.Smooth.Rd:25: Lost braces; missing escapes or markup?
    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
checkRd: (-1) SMC.Smooth.Rd:26: Lost braces; missing escapes or markup?
    26 | {logww} (their corresponding log weight).}
       | ^
Package required but not available: ‘GET’

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'tibble', 'tidyr', 'tidyselect', 'testthat'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dendextend', 'dplyr', 'ggplot2', 'ggraph', 'ggtree', 'hahmmr',
  'igraph', 'patchwork', 'pryr', 'purrr', 'scistreer', 'stringr',
  'tibble', 'tidygraph', 'tidyr', 'vcfR'

Packages suggested but not available for checking:
  'ggrastr', 'ggrepel', '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/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 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 ‘getting_started-vignette.Rmd’ using rmarkdown

Quitting from lines 26-36 [setup] (getting_started-vignette.Rmd)
Error: processing vignette 'getting_started-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘getting_started-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘getting_started-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
'LazyData' is specified without a 'data' directory
'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: 'igraph', 'huge'

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

Packages suggested but not available for checking:
  'distill', 'eurostat', 'ggalluvial', 'ggfittext', 'ggplot2',
  'ggpubr', 'ggrepel', 'kableExtra', 'readr', 'stringr', 'testthat',
  'tidyr'

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

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: ‘dae’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) xyz2R.Rd:31: Lost braces
    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
'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: ‘tibble’

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: ‘anyflights’
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'ggplot2', 'ggthemes', 'GGally',
  'forcats'
Running examples in ‘nzelect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GE2014
> ### Title: General Election Results 2014
> ### Aliases: GE2014
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # the following matches the results published at
> # http://www.electionresults.govt.nz/electionresults_2014/e9/html/e9_part1.html
> library(tidyr)
Error in library(tidyr) : there is no package called ‘tidyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
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 ‘README.Rmd’ using rmarkdown

Quitting from lines 47-59 [unnamed-chunk-2] (README.Rmd)
Error: processing vignette 'README.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘README.Rmd’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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', 'outbreaker2'

Packages suggested but not available for checking:
  'testthat', 'tigris', 'socialmixr'

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 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: 'stringr', 'tibble'

Packages suggested but not available for checking: 'RSQLite', '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: ‘igraph’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘oaqc_test.R’ [0s/1s]
Running the tests in ‘tests/oaqc_test.R’ failed.
Complete output:
  > stopifnot(require('oaqc'), require('igraph'),  getRversion() >= '3.4')
  Loading required package: oaqc
  Loading required package: igraph
  Error: require("igraph") is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'igraph'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2'

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'readr', '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:
  'testthat', 'ggplot2', 'patchwork'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(data.table)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘description-of-the-columns.Rmd’ using rmarkdown
--- finished re-building ‘description-of-the-columns.Rmd’

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

Quitting from lines 24-30 [setup] (obic_introduction.Rmd)
Error: processing vignette 'obic_introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘obic_introduction.Rmd’

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

Quitting from lines 37-46 [load binnenveld] (obic_score_aggregation.Rmd)
Error: processing vignette 'obic_score_aggregation.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘obic_score_aggregation.Rmd’

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

Quitting from lines 24-26 [setup] (obic_water_functions.Rmd)
Error: processing vignette 'obic_water_functions.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘obic_water_functions.Rmd’

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

Quitting from lines 62-82 [plot regime curve] (obic_workability.Rmd)
Error: processing vignette 'obic_workability.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building ‘obic_workability.Rmd’

SUMMARY: processing the following files failed:
  ‘obic_introduction.Rmd’ ‘obic_score_aggregation.Rmd’
  ‘obic_water_functions.Rmd’ ‘obic_workability.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', '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
Packages required but not available:
  'pec', 'purrr', 'dplyr', 'ggthemes', 'tidyr', 'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) OBMb.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages required but not available: 'bazar', 'dplyr', 'tibble'

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:
  'bib2df', 'dplyr', 'lubridate', 'rgbif', 'taxize', 'stringr',
  'ggplot2', 'tidyr', 'viridis', 'waffle'

Packages suggested but not available for checking: 'RefManageR', '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 suggested but not available for checking: ‘ggplot2’
Package required but not available: ‘stringr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
Packages required but not available:
  'ggplot2', 'thematic', 'purrr', 'ncmeta', 'dplyr'

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

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

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

Package suggested but not available for checking: ‘rio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'lubridate', 'ggplot2', 'ggedit', '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: ‘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/1s]
Running 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:
  'automap', 'lubridate', '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
Packages required but not available: 'stringr', 'orf'

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', 'adespatial'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
Running ‘testthat.R’ [0s/1s]
Running 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) ocsApiUserProvisioningManager.Rd:87: Lost braces
    87 |  \item{code{addToGroup(userid, groupid)}}{
       |            ^
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: 'usethis', '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', 'janitor', 'rio'

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

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

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: 'blob', 'hms'

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

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

Package suggested but not available for checking: ‘feasts’

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

Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'gt', 'RSQLite', 'stringr', 'testthat',
  'tibble', 'tidyselect', 'usethis'

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:
  'caret', 'ggplot2', 'tibble', 'ggthemes', 'tidymodels'

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', 'tibble', 'dplyr', 'tidyr'

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', 'tidyr'

Package suggested but not available for checking: ‘morse’

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: ‘sensitivity’

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: '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
Package required but not available: ‘gsheet’

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

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

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 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: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'benchmarkme', 'ggplot2', 'hexSticker', 'latex2exp', 'usethis',
  '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
Package required but not available: ‘dplyr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'doconv'
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:
  'doconv', 'ggplot2', 'magick', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(officer)
  +   library(xml2)
  + })
  Error in library(testthat) : there is no package called 'testthat'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'parsnip', 'poissonreg'

Packages suggested but not available for checking:
  'broom', 'recipes', 'testthat', 'tune', 'workflows', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'purrr', 'tidyr', 'tibble', 'ggpubr', 'ggExtra', 'tmap',
  '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
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                            ^
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                                                         ^
Packages required but not available:
  'dplyr', 'ggplot2', 'tigger', 'alakazam', 'stringr', 'tidyr'

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: ‘dplyr’

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

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

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'httptest', 'janitor', 'nominatimlite',
  'osmdata', 'testthat', 'tidyr'

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

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

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

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

Packages suggested but not available for checking: '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/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', 'car', 'dplyr', 'forcats', 'ggplot2', 'ggpubr', 'ggrepel',
  'lme4', 'lmerTest', 'readxl', 'rstatix', 'stringr', 'tibble',
  'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'arrow', 'clusterProfiler', 'FSA', 'ggplotify', 'kableExtra',
  'msigdbr', 'testthat', 'vdiffr'

VignetteBuilder package required for checking but not installed: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httr2', '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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'ggplot2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'opencpu', 'plotly', 'UpSetR'
Error(s) in re-building vignettes:
  ...
--- re-building ‘OmicNavigatorAPI.Rnw’ using Sweave
OmicNavigator R package version: 1.13.13
The app is not installed. Install it with installApp()
Installing study "ABC" in /home/hornik/tmp/scratch/RtmpCICjac/file3eb64370d1b648
Exporting study "ABC" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown <unknown@unknown>
Calculating pairwise overlaps. This may take a while...
Exported study to /home/hornik/tmp/scratch/RtmpCICjac/ONstudyABC

Error: processing vignette 'OmicNavigatorAPI.Rnw' failed with diagnostics:
 chunk 3 (label = test-data) 
Error in utils::install.packages(tmpPkgDir, lib = library, repos = NULL,  : 
  (converted from warning) installation of package ‘/home/hornik/tmp/scratch/RtmpCICjac/ONstudyABC’ had non-zero exit status

--- failed re-building ‘OmicNavigatorAPI.Rnw’

--- re-building ‘OmicNavigatorUsersGuide.Rnw’ using Sweave
OmicNavigator R package version: 1.13.13
The app is not installed. Install it with installApp()
Installing study "vignetteExample" in /home/hornik/tmp/scratch/RtmpkF5h9P/file3ebceb536fc245
Exporting study "vignetteExample" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown <unknown@unknown>
Calculating pairwise overlaps. This may take a while...
Exported study to /home/hornik/tmp/scratch/RtmpkF5h9P/ONstudyvignetteExample
Success!

Error: processing vignette 'OmicNavigatorUsersGuide.Rnw' failed with diagnostics:
 chunk 37 (label = cellTypeBoxGg) 
Error in library(ggplot2) : there is no package called ‘ggplot2’

--- failed re-building ‘OmicNavigatorUsersGuide.Rnw’

SUMMARY: processing the following files failed:
  ‘OmicNavigatorAPI.Rnw’ ‘OmicNavigatorUsersGuide.Rnw’

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: 'dplyr', 'ggplot2', '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:
  'kableExtra', '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 ‘Intro_to_omicsQC.Rmd’ using rmarkdown

Quitting from lines 20-22 [load_dependencies] (Intro_to_omicsQC.Rmd)
Error: processing vignette 'Intro_to_omicsQC.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘Intro_to_omicsQC.Rmd’

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

Error: Vignette re-building failed.
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.
Packages required but not available: 'dplyr', '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: 'broom', 'dplyr', 'purrr', '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’

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

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:
  'dbplyr', 'dplyr', 'snakecase', '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/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: 'dplyr', 'gt'

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', 'ggfortify', 'ggplot2', 'tidyr', 'broom', 'FSA',
  'rstatix', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RoeDeerMass-simulation.Rnw’ using Sweave

Error: processing vignette 'RoeDeerMass-simulation.Rnw' failed with diagnostics:
 chunk 6 (label = testTF) 
Error in loadNamespace(x) : there is no package called ‘lme4’

--- failed re-building ‘RoeDeerMass-simulation.Rnw’

SUMMARY: processing the following file failed:
  ‘RoeDeerMass-simulation.Rnw’

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

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

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

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

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

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

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:
  'rstan', 'tibble', 'dplyr', 'tidyr', 'purrr', 'furrr', 'stringr',
  'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'sva', 'GenomicFeatures', 'org.Hs.eg.db',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'tidyverse', 'TCGAbiolinks'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) oncotree.fit.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available:
  'dplyr', 'ggplot2', 'caret', 'DALEX', 'readr', 'pdp', 'tidyr'

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

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

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

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

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', 'tidyr'

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

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

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', 'survminer'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'doctest', '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) one_sample.Rd:40: Lost braces; missing escapes or markup?
    40 | In two sided or one sided interval estimation of \code{sigma^2} of one normal sample, {side} is a parameter used to control whether to compute two sided or one sided interval estimation. When computing the one sided upper limit, input \code{side = -1}; when computing the one sided lower limit, input \code{side = 1}; when computing the two sided limits, input \code{side = 0} (default).
       |                                                                                       ^
Packages required but not available: 'car', 'ggplot2'

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

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: ‘VIM’

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', 'plotly'
Packages required but not available: 'dplyr', 'readxl', '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: ‘sqldf’

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: 'readr', 'tibble'

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

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: ‘gt’

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

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

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

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

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

Packages suggested but not available for checking:
  'keyATM', 'testthat', 'dplyr', 'stm', 'stringr', 'shinytest2'

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
Packages required but not available:
  'caret', 'dplyr', 'forecast', 'furrr', 'ggplot2', 'imputeTS',
  'lubridate', 'purrr', '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 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', 'progress', 'labelled', '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’
Packages suggested but not available for checking: 'testthat', '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
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'ggspatial', 'ggtext', 'lubridate',
  'openair', 'purrr', 'rosm', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘worldmet’

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

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.
Packages required but not available: 'progress', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'purrr', '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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'progress', 'purrr', 'tibble', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
License stub is invalid DCF.
GNU make is a SystemRequirements.
Package required but not available: ‘vctrs’

Packages suggested but not available for checking: 'arrow', 'haven'

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

Packages suggested but not available for checking:
  'testthat', 'R2ucare', 'secrlinear'

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: 'ckanr', 'readxl', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'ggiraph', 'ggplot2', 'purrr', 'tidyr', '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.
Package required but not available: ‘ggplot2’

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

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

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

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

Packages suggested but not available for checking:
  'broom', 'dplyr', 'forcats', 'lubridate', 'testthat', 'tidyr',
  'tidytext', 'stringr'

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

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

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

Package suggested but not available for checking: ‘httptest’

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: 'readxl', 'stringr', 'usethis'

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', 'farff'
Packages required but not available: 'MSEtool', 'DLMtool', 'SAMtool'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'roxygen2', 'lme4', 'testthat', 'umx', 'ifaTools', 'reshape2',
  'ggplot2'
GNU make is a SystemRequirements.
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mxEvaluateOnGrid
> ### Title: Evaluate an algebra on an abscissa grid and collect column
> ###   results
> ### Aliases: mxEvaluateOnGrid
> 
> ### ** Examples
> 
> library(OpenMx)
> 
> test2 <- mxModel("test2",
+ 	mxMatrix(values=1.1, nrow=1, ncol=1, free=TRUE, name="thang"),
+ 	mxMatrix(nrow=1, ncol=1, labels="abscissa1", free=TRUE, name="currentAbscissa"),
+ 	mxMatrix(values=-2:2, nrow=1, ncol=5, name="abscissa",
+ 		 dimnames=list(c('abscissa1'), NULL)),
+ 	mxAlgebra(rbind(currentAbscissa + thang, currentAbscissa * thang), name="stuff"),
+ 	mxAlgebra(mxEvaluateOnGrid(stuff, abscissa), name="grid"))
> 	
> test2 <- mxRun(test2)
Running test2 with 2 parameters
> omxCheckCloseEnough(test2$grid$result, matrix(c(-1:3 + .1, -2:2 * 1.1), ncol=5, nrow=2,byrow=TRUE))
Error in omxCheckCloseEnough(test2$grid$result, matrix(c(-1:3 + 0.1, -2:2 *  : 
  Please install.packages(testthat) and try again
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
mxBootstrapEval       5.512  0.158  11.012
mxCheckIdentification 4.184  0.068   5.605
Running ‘testthat.R’ [0s/1s]
Running 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: ‘openNLPmodels.en’
Packages required but not available:
  'dplyr', 'stringr', 'reshape2', 'igraph', 'tidyr', 'tidyverse'

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', 'tidyr', 'dplyr', '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:
  'ggmap', 'ggplot2', 'magick', 'RPresto'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘engine.R’ [0s/1s]
  Comparing ‘engine.Rout’ to ‘engine.Rout.save’ ...4d3
< Linking to: OpenSSL 3.2.2-dev 
  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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geiger', 'knitcitations', 'paleotree', 'rotl', 'stringr', 'taxize',
  'usethis'

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

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: 'InterVA5', 'InSilicoVA', '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', 'mschart', 'testthat', '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
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 suggested but not available for checking: 'testthat', 'caret'
checkRd: (-1) loss.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mixture.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mixture.Rd:34: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running 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:
  'AdaptGauss', 'DataVisualizations', 'DistributionOptimization',
  'mixtools', 'ggplot2', 'dplyr', 'mixAK', 'ClusterR'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'hopbyhop', 'endtoend'
checkRd: (-1) MonteCarlo.Rd:23: Lost braces
    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
Packages required but not available: 'tibble', 'tidytree', 'ggplot2'

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

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

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: ‘reshape2’

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: 'ggplot2', 'purrr', 'dplyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
checkRd: (-1) optimal_holdout_size.Rd:30: Lost braces; missing escapes or markup?
    30 | List/data frame of dimension (number of evaluations) x (4 + n_par) containing input data and results. Columns \code{size} and \code{cost} are optimal holdout size and cost at this size respectively. Parameters N, k1, theta.1, theta.2,...,theta.{n_par} are input data.
       |                                                                                                                                                                                                                                                     ^
checkRd: (-1) drawdesign.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:44: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'did', 'dplyr', 'purrr', '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:
  'cowplot', 'ggrepel', 'reshape2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) gnu_style.Rd:24: Lost braces
    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
Running ‘testthat.R’ [0s/1s]
Running 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: ‘gurobi’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'nloptr', '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', 'tibble'

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

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

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

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', 'dplyr'

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

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:
  > # 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
  > 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("OptimModel")
  Error in test_check("OptimModel") : could not find function "test_check"
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘OptimModel_vignette.Rmd’ using rmarkdown

Quitting from lines 219-254 [unnamed-chunk-4] (OptimModel_vignette.Rmd)
Error: processing vignette 'OptimModel_vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘OptimModel_vignette.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'ggplot2'
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
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: ‘nloptr’

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:
  > # 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:
  'keras', 'tsutils', 'readxl', 'tibble', 'tensorflow', 'forecast',
  'dplyr', 'caretForecast', 'kknn', 'FactoMineR', 'factoextra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'tidyverse'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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:
  'RItools', 'testthat', 'roxygen2', 'arm', 'rrelaxiv'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'stringr', 'testthat'
Running ‘run-all.R’ [0s/1s]
  Running ‘test_help.R’ [0s/1s]
  Comparing ‘test_help.Rout’ to ‘test_help.Rout.save’ ... OK
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: ‘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: 'gurobi', '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: 'cobalt', 'twang'

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', 'readr', 'purrr', 'reshape2', 'stringr', 'rvest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘orbweaver/libs/orbweaver.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:
  > # 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:
  'brms', 'transformr', 'dplyr', 'ggplot2', 'gganimate', 'tidyr'

Packages suggested but not available for checking:
  'gt', 'haven', 'stringr', 'Hmisc', 'ggthemes', 'glmmTMB', 'mice'

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.
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
Package required but not available: ‘RSQLite’

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
checkRd: (-1) internal.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:70: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'DESeq2', 'devtools', 'dclone'

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rms'
Packages suggested but not available for checking: 'lme4', 'testthat'
checkRd: (-1) minK.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:15: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘RLRsim’

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', 'tidyselect', 'tibble', 'tidyr', 'dplyr',
  'purrr', 'ggrepel'

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

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', 'readr', 'tidyr', 'ggplot2', 'stringr'

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: ‘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: 'readr', '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:
  'ggthemes', 'ggplot2', 'lubridate', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Packages suggested but not available for checking:
  'testthat', 'stringr', 'forecast'
Running examples in ‘origami-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cross_validate
> ### Title: Main Cross-Validation Function
> ### Aliases: cross_validate
> 
> ### ** Examples
> 
> ###############################################################################
> # This example explains how to use the cross_validate function naively.
> ###############################################################################
> data(mtcars)
> 
> # resubstitution MSE
> r <- lm(mpg ~ ., data = mtcars)
> mean(resid(r)^2)
[1] 4.609201
> 
> # function to calculate cross-validated squared error
> cv_lm <- function(fold, data, reg_form) {
+   # get name and index of outcome variable from regression formula
+   out_var <- as.character(unlist(stringr::str_split(reg_form, " "))[1])
+   out_var_ind <- as.numeric(which(colnames(data) == out_var))
+ 
+   # split up data into training and validation sets
+   train_data <- training(data)
+   valid_data <- validation(data)
+ 
+   # fit linear model on training set and predict on validation set
+   mod <- lm(as.formula(reg_form), data = train_data)
+   preds <- predict(mod, newdata = valid_data)
+ 
+   # capture results to be returned as output
+   out <- list(
+     coef = data.frame(t(coef(mod))),
+     SE = ((preds - valid_data[, out_var_ind])^2)
+   )
+   return(out)
+ }
> 
> # replicate the resubstitution estimate
> resub <- make_folds(mtcars, fold_fun = folds_resubstitution)[[1]]
> resub_results <- cv_lm(fold = resub, data = mtcars, reg_form = "mpg ~ .")
Error in loadNamespace(x) : there is no package called ‘stringr’
Calls: cv_lm ... 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 ‘generalizedCV.Rmd’ using rmarkdown

Quitting from lines 118-120 [load_pkgs] (generalizedCV.Rmd)
Error: processing vignette 'generalizedCV.Rmd' failed with diagnostics:
there is no package called 'stringr'
--- failed re-building ‘generalizedCV.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'purrr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > testthat::test_check("origin")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘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) distsumlpmin.Rd:69: Lost braces
    69 |   \code{Véase}{Vease} \enc{también}{tambien} \code{\link{distsummin}}, \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |               ^
checkRd: (-1) distsummin.Rd:80: Lost braces
    80 | \code{Véase}{Vease} \enc{también}{tambien} \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |             ^
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: 'rms', 'Hmisc', 'benchmarkme'

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

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 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) hillEquation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:91-93: Lost braces in \itemize; \value handles \item{}{} directly
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) polynomial.derivatives.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:21: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘googleCloudVisionR’

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

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:
  > # 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: ‘ePCR’
checkRd: (-1) oscar.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
checkRd: (-1) oscar.control.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
'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: ‘mc2d’

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

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: 'dplyr', '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: 'Luminescence', 'ggplot2', 'ggpubr'

Package suggested but not available for checking: ‘kableExtra’

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

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: ‘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: ‘OpenStreetMap’

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 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’

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: ‘netmeta’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 120-124 [unnamed-chunk-11] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'netmeta'
--- 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/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: 'hypervolume', 'ggplot2', '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: ‘pec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'janitor', 'ggiraphExtra', 'dplyr', 'ggplot2', 'ggrepel', '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: ‘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: 'janitor', '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', 'mice', 'missMDA', 'FactoMineR', 'StatMatch'

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.
Packages required but not available: 'ggplot2', 'latex2exp'

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

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

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

Packages suggested but not available for checking:
  'IRdisplay', 'mockery', 'stringr', 'IRkernel'

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

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

Packages suggested but not available for checking:
  'testthat', 'igraph', 'epicontacts', 'adegenet'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nipah_malaysia
> ### Title: Nipah in Malaysia and Sinagapore, 1997-1999
> ### Aliases: nipah_malaysia
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## show first few weeks of Dengue incidence
> head(nipah_malaysia)
        date perak negeri_sembilan selangor singapore
1 1997-01-04     0               0        0         0
2 1997-01-11     1               0        0         0
3 1997-01-18     0               0        0         0
4 1997-01-25     1               0        0         0
5 1997-02-01     1               0        0         0
6 1997-02-08     0               0        0         0
> 
> ## convert data to incidence object and plot epicurve using the incidence package
> library(incidence)
Error in library(incidence) : there is no package called ‘incidence’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running 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', 'forcats', 'ggplot2', 'testthat', 'tidyr', 'stringr'
checkRd: (-1) fmat.Rd:15: Lost braces; missing escapes or markup?
    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
checkRd: (-1) fmat.Rd:24: Lost braces; missing escapes or markup?
    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
checkRd: (-1) fmat.Rd:25: Lost braces; missing escapes or markup?
    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
checkRd: (-1) fmat.Rd:26: Lost braces; missing escapes or markup?
    26 | produce {eUH, eUO}.
       |         ^
checkRd: (-1) middleearth.Rd:14: Lost braces; missing escapes or markup?
    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
Running ‘testthat.R’ [0s/1s]
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 ‘intro-to-outcomerate.Rmd’ due to unavailable dependencies:
  'dplyr', 'ggplot2', 'tidyr', 'stringr'
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: 'airt', 'EstCRM'

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', 'dplyr', 'tidyr', 'forcats', 'HDoutliers', 'cellWise',
  'GGally'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'mockery'
'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', 'ggrepel', 'ggvenn', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'pkgdown', '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:
  'twang', 'EnvStats', 'devtools', 'dplyr', 'ggplot2', 'ggrepel',
  'metR', 'purrr', 'progress', 'tibble', 'tidyselect'

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

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', 'ggplot2', 'ggridges'

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(ox)
  > testthat::test_check("ox")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Note: skipping ‘ox-examples.Rmd’ due to unavailable dependencies: 'dplyr'
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.
Package required but not available: ‘tibble’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggiraph', 'ggplot2'
Packages required but not available:
  'readxl', 'stringr', 'reshape2', 'lme4', 'survminer', 'systemfit',
  'IPDFileCheck', 'valueEQ5D', 'car', 'ggplot2', 'broom', 'effects',
  'dplyr', 'tidyr', 'haven', 'ggpubr', 'labelled', '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: 'usethis', 'roxygen2'

Package suggested but not available for checking: ‘testthat’

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 suggested but not available for checking:
  'devtools', 'mockery', 'testthat'
Running ‘test-cranlike-repositories.R’ [3s/6s]
  Running ‘testthat.R’ [0s/1s]
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’
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
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:
  'igraph', 'dplyr', 'ggplot2', 'ggrepel'

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

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

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'

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pagenum
> ### Title: Put Page Numbers on Graphics
> ### Aliases: pagenum setPagenum getPagenum
> 
> ### ** Examples
> 
> # base graphics
> setPagenum(1)
> plot(Sepal.Length~Sepal.Width, data=iris, col=Species, pch=19)
> pagenum()
> 
> # lattice, date
> setPagenum(getPagenum()+1) # Manual increment
> require(lattice)
Loading required package: lattice
> xyplot(Sepal.Length~Sepal.Width, data=iris, groups=Species)
> pagenum(date=TRUE)
> 
> # ggplot2, top-right
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> ggplot(iris, aes(x=Sepal.Width, y=Sepal.Length,
+   color=Species)) + geom_point() + theme_classic()
Error in ggplot(iris, aes(x = Sepal.Width, y = Sepal.Length, color = Species)) : 
  could not find function "ggplot"
Execution halted
Running ‘testthat.R’ [0s/1s]
Running 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', 'WikidataR'
Running ‘testthat.R’ [0s/1s]
Running 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: 'igraph', 'sccore'

Packages suggested but not available for checking:
  'AnnotationDbi', 'dplyr', 'ggplot2', 'GO.db', 'org.Dr.eg.db',
  'org.Hs.eg.db', 'org.Mm.eg.db', '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’

Package suggested but not available for checking: ‘patchwork’

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 suggested but not available for checking: 'igraph', 'alr4'
Package required but not available: ‘mcprofile’

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 suggested but not available for checking: ‘testthat’
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Ch.Rd:297: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:214: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:215: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:109: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:110: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:336: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:337: Lost braces in \enumerate; meant \describe ?
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: ‘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: ‘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: ‘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: ‘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: ‘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: 'mockery', 'testthat'
Packages required but not available:
  'tibble', 'dplyr', 'ggplot2', 'forcats', 'assertr', 'ggrepel',
  'tidyr', '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: ‘h3jsr’

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

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

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

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/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’

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 ‘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
Packages required but not available: 'phangorn', 'phytools'

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’

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

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

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

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

Packages suggested but not available for checking:
  'pkgdown', 'testthat', 'dplyr', 'gt', 'biscale', 'patchwork',
  'MetBrewer', 'nord'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_poke
> ### Title: Add a pokemon palette to a ggplot2 colour or fill scale.
> ### Aliases: scale_color_poke scale_colour_poke scale_fill_poke
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking:
  'tibble', 'ggplot2', 'dplyr', 'tidyr', 'recipes'
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/1s]
Running 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', 'viridis'
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', 'reshape2', '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', '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: 'readxl', 'readmoRe', 'robustHD'

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

Package suggested but not available for checking: ‘testthat’

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)
  Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 35 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pamr.Rcheck/00install.out’ for details.
* used Fortran compiler: ‘GNU Fortran (Debian 13.2.0-25) 13.2.0’
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'tidyr', 'readr', 'PAMmisc', '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: 'org.Hs.eg.db', 'igraph', '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’

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', 'Epi', 'rms', 'forecast'
checkRd: (-1) Pandoc.convert.Rd:42: Lost braces
    42 | Calling John MacFarlane's great program to convert specified file (see \code{f} parameter below) or character vector {see \code{text} paramater} to other formats like \code{HTML}, \code{pdf}, \code{docx}, \code{odt} etc.
       |                                                                                                                      ^
Packages suggested but not available for checking:
  'gh', 'testthat', 'tibble'
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', 'readODS', 'readr', 'readxl'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
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’

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', 'dplyr', 'ggplot2', 'jtools', 'lmerTest', 'purrr', 'stringr',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'car', 'geepack', 'skimr', 'testthat'

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) hvidovre.Rd:11: Lost braces
    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
checkRd: (-1) hvidovre.Rd:25: Lost braces
    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
checkRd: (-1) hvidovre.Rd:26: Lost braces
    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
Package suggested but not available for checking: ‘lme4’
Packages suggested but not available for checking:
  'dplyr', 'magick', '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 ‘PS1_Cat.Rmd’ using rmarkdown

Quitting from lines 18-21 [setup] (PS1_Cat.Rmd)
Error: processing vignette 'PS1_Cat.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘PS1_Cat.Rmd’

--- re-building ‘PS1_Images.Rmd’ using rmarkdown

Quitting from lines 19-21 [setup] (PS1_Images.Rmd)
Error: processing vignette 'PS1_Images.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building ‘PS1_Images.Rmd’

SUMMARY: processing the following files failed:
  ‘PS1_Cat.Rmd’ ‘PS1_Images.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘tibble’
Note: skipping ‘panta-rhei.Rmd’ due to unavailable dependencies: 'tibble'
Package required but not available: ‘broom’

Packages suggested but not available for checking:
  'afex', 'BayesFactor', 'car', 'dplyr', 'ggforce', 'ggplot2',
  'latex2exp', 'lme4', 'lmerTest', 'MBESS', 'skimr', 'testthat'

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

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’

Package which this enhances but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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’
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## testthat.R
  > ##
  > ## Copyright (C)  2017  Alexander Eckert
  > ##
  > ## This file is part of parallelDist.
  > ##
  > ## parallelDist 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.
  > ##
  > ## parallelDist 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 parallelDist. If not, see <http://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Note: skipping ‘parallelDist.Rnw’ due to unavailable dependencies:
  'ggplot2'
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:
  'BatchJobs', 'batchtools', 'testthat'
Running ‘run-all.R’ [0s/0s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > # FIXME: R CMD check does not run on true batch systems, but maybe it does not have to
  > # we can check there with 'make test' and run 'make check' locally
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘pcalg’
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)
> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
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:
  'AER', 'afex', 'BayesFactor', 'BayesFM', 'blme', 'brms', 'broom',
  'cAIC4', 'car', 'cgam', 'cplm', 'drc', 'EGAnet', 'epiR',
  'factoextra', 'FactoMineR', 'faraway', 'geepack', 'ggplot2',
  'glmmTMB', 'gt', 'haven', 'Hmisc', 'ivreg', 'lme4', 'lmerTest',
  'logistf', 'M3C', 'mediation', 'merDeriv', 'metaBMA', 'mice', 'mmrm',
  'nestedLogit', 'panelr', 'pbkrtest', 'posterior', 'PROreg', 'rms',
  'rstanarm', 'see', 'testthat', 'tidyselect'
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(parameters)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'GGally', 'ggplot2', 'reshape2', 'testthat'
checkRd: (-1) getParamNr.Rd:15: Lost braces
    15 | Default is code{FALSE}.}
       |                ^
checkRd: (-1) getRequirements.Rd:16: Lost braces
    16 | code{TRUE}.}
       |     ^
checkRd: (-1) sampleValue.Rd:15: Lost braces; missing escapes or markup?
    15 | Default is code {FALSE}.}
       |                 ^
checkRd: (-1) sampleValues.Rd:18: Lost braces; missing escapes or markup?
    18 | Default is code {FALSE}.}
       |                 ^
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: ‘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:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘igraph’
Packages required but not available: 'forecast', '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: 'readr', 'purrr'

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:
  'beepr', 'ggplot2', 'dplyr', '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
Note: skipping ‘Simulating-Power.Rmd’ due to unavailable dependencies:
  'ggplot2', 'dplyr'
Packages required but not available: 'ggplot2', 'ggpubr'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking: 'testthat', '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 suggested but not available for checking: 'stringr', 'testthat'
Running examples in ‘parcr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: store
> ### Title: Store and retrieve objects
> ### Aliases: store retrieve
> 
> ### ** Examples
> 
> parse_nr <- function(line) {
+   m <- stringr::str_extract(line, "number=(\\d+)", group=1)
+   if (is.na(m)) list()
+   else store("nr", as.numeric(m))
+ }
> 
> p <- function() {
+   match_s(parse_nr) %then%
+     exactly(retrieve("nr"), literal("A"))
+ }
> 
> p()(c("number=3", "A", "A", "A")) # success
Error in loadNamespace(x) : there is no package called ‘stringr’
Calls: <Anonymous> ... 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Creating_parser_combinators.Rmd’ using rmarkdown

Quitting from lines 567-568 [unnamed-chunk-31] (Creating_parser_combinators.Rmd)
Error: processing vignette 'Creating_parser_combinators.Rmd' failed with diagnostics:
there is no package called 'stringr'
--- failed re-building ‘Creating_parser_combinators.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'DiagrammeR', 'dplyr', 'stringr', 'igraph'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) PPS.fit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forbes400.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forbes400.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:11: 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:
  > 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: ‘raqs’

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/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: ‘nloptr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ast2ast', 'dfdr'

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

Package suggested but not available for checking: ‘testthat’

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

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: '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:
  'purrr', 'readr', 'tidyr', 'dplyr', 'tibble', 'pillar', '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', '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: ‘dplyr’

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

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

Packages suggested but not available for checking:
  'C50', 'bench', 'dials', 'ggrepel', 'keras', 'kknn', 'modeldata',
  'sparklyr', 'tensorflow', 'testthat'

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

Package suggested but not available for checking: ‘AER’

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

Quitting from lines 39-72 [IV1] (PartialNetwork_vignette.Rmd)
Error: processing vignette 'PartialNetwork_vignette.Rmd' failed with diagnostics:
there is no package called 'CDatanet'
--- failed re-building ‘PartialNetwork_vignette.Rmd’

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

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

Package suggested but not available for checking: ‘ggraph’

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

Packages suggested but not available for checking: 'ggcorrplot', '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: ‘regtools’

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', 'dplyr', 'purrr', 'tibble', 'ggplot2', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'pillar', '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: 'pmml', 'AER'
Note: skipping ‘constparty.Rnw’ due to unavailable dependencies: 'pmml'
Note: skipping ‘mob.Rnw’ due to unavailable dependencies: 'AER'
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: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) PAS-package.Rd:30: Lost braces
    30 |     {\code{bin model}}{\cr Zhiqiu Hu, Zhiquan Wang, and Shizhong Xu (2012) An infinitesimal model for quantitative trait genomic value prediction. PloS ONE 7: e41336.}
       |                       ^
Package suggested but not available for checking: ‘MKmisc’
Packages required but not available:
  'ggplot2', 'dplyr', 'GGally', 'progress', 'plotly'

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

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

Quitting from lines 32-40 [intro] (passport.Rmd)
Error: processing vignette 'passport.Rmd' failed with diagnostics:
there is no package called 'gapminder'
--- failed re-building ‘passport.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', '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: 'ggplot2', 'glmmTMB', 'lme4'

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: ‘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 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: 'lubridate', 'dplyr', 'progress'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', '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
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) as_config.Rd:32: Lost braces; missing escapes or markup?
    32 | with `{config}` package, which requires existence of default key.
       |       ^
checkRd: (-1) as_config.Rd:28: Lost braces; missing escapes or markup?
    28 | list compatible with `{config}` package
       |                       ^
'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:
  'AnnotationDbi', 'org.Hs.eg.db', 'ggplot2', 'ggraph', 'ggupset',
  'ggkegg', 'igraph', 'msigdbr'

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'CodelistGenerator', 'odbc', 'ggplot2', 'RPostgres',
  'dbplyr', 'gt'

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

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

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:
  'igraph', 'jetset', 'SelectBoost', 'tnet', 'WGCNA'

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

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

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

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 suggested but not available for checking: 'mockery', '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’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'DescTools', 'dplyr'

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: 'ggplot2', 'ggpubr'

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

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

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'broom', '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
'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: 'purrr', '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
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘ggplot2’

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

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: 'igraph', 'ggm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘exact2x2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running 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: 'optmatch', '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 ‘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:
  'ggplot2', 'tibble', 'ggrepel', 'dplyr'

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', 'readr'

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: ‘gMOIP’

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

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

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

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

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

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: ‘bigstatsr’

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: ‘roxygen2’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mvSLOUCH', 'phangorn'

Package suggested but not available for checking: ‘geiger’

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

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', 'ggtree', 'cowplot', 'mvSLOUCH'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getPCRAData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:29: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘ggplot2’

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

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.
'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 ‘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:
  'pcutils', 'dplyr', 'ggplot2', 'ggrepel', 'reshape2', 'tibble',
  'ggpubr', 'ggnewscale'

Packages suggested but not available for checking:
  'ggpmisc', 'NST', 'aplot', 'mixOmics', 'phyloseq',
  'phyloseqGraphTest', 'plotly', 'Hmisc', 'patchwork', 'tidytree',
  'ggtree', 'ggtreeExtra', 'vctrs', 'DESeq2', 'MetaNet', 'zetadiv',
  'ggforce', 'readxl'

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

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

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', 'reshape2', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'ggpubr', 'kableExtra', 'ggsci', 'readr', 'ggalluvial', 'gghalves',
  'ggspatial', 'magick', 'ggimage', 'ggpmisc', 'UpSetR', 'igraph',
  'plotly', 'stringr', 'ggraph', 'ggrepel', 'treemap', 'devtools',
  'rio', 'styler', 'aplot', 'ggbeeswarm', 'ggVennDiagram'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Package required but not available: ‘rvest’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'PythonInR', 'RSQLite'
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’
Running ‘poppler.R’ [0s/1s]
  Comparing ‘poppler.Rout’ to ‘poppler.Rout.save’ ...4d3
< Using poppler version 24.02.0
  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', 'purrr', 'readxl', 'stringr', 'tibble', 'tidyr',
  'tidyselect'

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

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

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

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

Packages suggested but not available for checking:
  'adabag', 'AmesHousing', 'C50', 'caret', 'Cubist', 'dplyr', 'keras',
  'vip'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'pillar', 'testthat', 'vdiffr'
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 suggested but not available for checking:
  'ggplot2', 'reshape2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright 2015 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of PDQutils.
  > #
  > # PDQutils 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.
  > #
  > # PDQutils 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 PDQutils.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2015.06.06
  > # Copyright: Steven E. Pav, 2015-2015
  > # 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘PDQutils.Rnw’ using knitr
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'rsnak'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'testit'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.


Quitting from lines 734-750 [testit] (PDQutils.Rnw)
Error: processing vignette 'PDQutils.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘PDQutils.Rnw’

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

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

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', 'ggplot2', 'reshape2', 'viridis', 'ggthemes'
Specified C++11: please drop specification unless essential
checkRd: (-1) pdkMeans.Rd:63: Lost braces
    63 | \cite{C18}{pdSpecEst} for more details. Note that this comes at the cost of increased computation time in comparison to one
       |           ^
'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: 'monobin', 'dplyr'

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

Packages suggested but not available for checking:
  'leaflet.extras', 'gganimate', 'infer', 'moderndive', 'readr',
  'ggplot2', 'forcats'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
Packages suggested but not available for checking: 'testthat', 'ggplot2'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running examples in ‘PeakSegDisk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PeakSegFPOP_df
> ### Title: PeakSeg penalized solver for data.frame
> ### Aliases: PeakSegFPOP_df
> 
> ### ** Examples
> 
> 
> ## Simulate a sequence of Poisson count data.
> sim.seg <- function(seg.mean, size.mean=15){
+   seg.size <- rpois(1, size.mean)
+   rpois(seg.size, seg.mean)
+ }
> set.seed(1)
> seg.mean.vec <- c(1.5, 3.5, 0.5, 4.5, 2.5)
> z.list <- lapply(seg.mean.vec, sim.seg)
> z.rep.vec <- unlist(z.list)
> 
> ## Plot the simulated data sequence.
> if(require(ggplot2)){
+   count.df <- data.frame(
+     position=seq_along(z.rep.vec),
+     count=z.rep.vec)
+   gg.count <- ggplot()+
+     geom_point(aes(
+       position, count),
+       shape=1,
+       data=count.df)
+   gg.count
+ }
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> 
> ## Plot the true changes.
> n.segs <- length(seg.mean.vec)
> seg.size.vec <- sapply(z.list, length)
> seg.end.vec <- cumsum(seg.size.vec)
> change.vec <- seg.end.vec[-n.segs]+0.5
> change.df <- data.frame(
+   changepoint=change.vec)
> gg.change <- gg.count+
+   geom_vline(aes(
+     xintercept=changepoint),
+     data=change.df)
Error: object 'gg.count' not found
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples.Rnw’ using knitr

Quitting from lines 209-213 [unnamed-chunk-4] (Examples.Rnw)
Error: processing vignette 'Examples.Rnw' failed with diagnostics:
object 'gg.change' not found
--- failed re-building ‘Examples.Rnw’

--- re-building ‘Spatial_correlation.Rmd’ using knitr
--- finished re-building ‘Spatial_correlation.Rmd’

--- re-building ‘Worst_case.Rmd’ using knitr
--- finished re-building ‘Worst_case.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'penaltyLearning'
Running examples in ‘PeakSegDP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chr11ChIPseq
> ### Title: ChIP-seq aligned read coverage for 4 samples on a subset of
> ###   chr11
> ### Aliases: chr11ChIPseq
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(chr11ChIPseq)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running 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: ‘penaltyLearning’

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: ‘penaltyLearning’

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: 'rms', 'riskRegression'

Package suggested but not available for checking: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'dplyr', 'ggplot2', 'lubridate', 'qwraps2', '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: 'ggpubr', 'qwraps2'

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:
  > # 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: ‘lme4’

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

Quitting from lines 94-97 [unnamed-chunk-3] (demo.Rmd)
Error: processing vignette 'demo.Rmd' failed with diagnostics:
there is no package called 'DiagrammeR'
--- failed re-building ‘demo.Rmd’

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

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

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

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: ‘car’
checkRd: (-1) variogramGuess.Rd:94: Lost braces
    94 | Method \code{"b"} was proposed by \doi{10.1016/0098-3004(95)00095-X}{Jian et al. (1996)} and
       |                                                                     ^
checkRd: (-1) variogramGuess.Rd:98: Lost braces
    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
checkRd: (-1) variogramGuess.Rd:100: Lost braces
   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotESDA
> ### Title: Plots for exploratory spatial data analysis (ESDA)
> ### Aliases: plotESDA
> 
> ### ** Examples
> 
> if (all(require(sp), require(gstat))) {
+   data(meuse, package = "sp")
+   p <- plotESDA(z = meuse$zinc, lat = meuse$y, lon = meuse$x)
+ }
Loading required package: sp
Loading required package: gstat
Loading required namespace: car
Failed with error:  ‘there is no package called ‘car’’
Error in plotHD(z, HD = "over", stats = FALSE, asp = 1, xlab = "z", col = c("skyblue",  : 
  car package is missing
Calls: plotESDA -> plotHD
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:
  'rvest', 'lubridate', 'readxl', 'readr', 'echarts4r'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ibdsim2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'igraph', 'kableExtra', '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 ‘pedtools.Rmd’ using rmarkdown

Quitting from lines 17-25 [setup] (pedtools.Rmd)
Error: processing vignette 'pedtools.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘pedtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'httr2', '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 suggested but not available for checking: ‘adegenet’
Running examples in ‘pegas-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hap.div
> ### Title: Haplotype Diversity
> ### Aliases: hap.div hap.div.haplotype hap.div.DNAbin
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(woodmouse)
> hap.div(woodmouse) # all haplotypes are unique
[1] 1
> 
> ## neuraminidase sequences from the 2009 H1N1 data (delivered with adegenet):
> fl <- system.file("files/pdH1N1-NA.fasta", package = "adegenet")
> H1N1.NA <- read.dna(fl, "fasta")
Warning in file(con, "rb") :
  file("") only supports open = "w+" and open = "w+b": using the former
Error in readBin(file, "raw", file.size(file)) : 
  can only read from a binary connection
Calls: read.dna -> read.FASTA -> readBin
Execution halted
Packages required but not available:
  'tidyverse', 'ggplot2', 'dplyr', 'purrr', 'stringr', '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 ‘testthat.R’ [0s/1s]
Running 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', 'treemap', 'visdat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘download.Rmd’ using rmarkdown
--- finished re-building ‘download.Rmd’

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

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

Quitting from lines 22-25 [setup] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘intro.Rmd’

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

SUMMARY: processing the following file failed:
  ‘intro.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: 'rstan', 'ggplot2'

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

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

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’
Package suggested but not available for checking: ‘tidyverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘penalizedclr.Rmd’ using rmarkdown

Quitting from lines 61-63 [unnamed-chunk-4] (penalizedclr.Rmd)
Error: processing vignette 'penalizedclr.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘penalizedclr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘globaltest’
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
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', 'purrr', 'riskRegression'

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

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

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

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

Package suggested but not available for checking: ‘plotly’

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

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'reshape2'

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/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
checkRd: (-1) mc3_pep.Rd:53: Lost braces; missing escapes or markup?
    53 | is not 2^{p} but the number of unique models `visited' by the 
       |          ^
Packages required but not available: 'dplyr', '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
Packages required but not available: 'stringr', '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
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', 'stringr', 'caret'

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

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', 'testthat', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', '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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Perc.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Perc.Rcheck/vign_test/Perc/vignettes/Perc_files/figure-html/unnamed-chunk-12-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18409 bytes
Input file size = 18511 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 13049
  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 = 13049

Output IDAT size = 13049 bytes (5360 bytes decrease)
Output file size = 13127 bytes (5384 bytes = 29.09% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Perc.Rcheck/vign_test/Perc/vignettes/Perc_files/figure-html/unnamed-chunk-13-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18293 bytes
Input file size = 18395 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12855
  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 = 12855

Output IDAT size = 12855 bytes (5438 bytes decrease)
Output file size = 12933 bytes (5462 bytes = 29.69% decrease)


Quitting from lines 179-181 [unnamed-chunk-15] (Perc.Rmd)
Error: processing vignette 'Perc.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘Perc.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Hmisc', 'ggplot2', 'plotly', 'ggpubr'
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) Return.portfolio.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:110-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:114-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:119-122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:123-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:130-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Running examples in ‘PerformanceAnalytics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Omega
> ### Title: calculate Omega for a return series
> ### Aliases: Omega
> 
> ### ** Examples
> 
> 
>     data(edhec)
>     Omega(edhec)
               Convertible Arbitrage CTA Global Distressed Securities
Omega (L = 0%)               2.79388   1.573902              2.794442
               Emerging Markets Equity Market Neutral Event Driven
Omega (L = 0%)         1.700861              4.499562     2.636198
               Fixed Income Arbitrage Global Macro Long/Short Equity
Omega (L = 0%)               3.312118     2.834636          2.253459
               Merger Arbitrage Relative Value Short Selling Funds of Funds
Omega (L = 0%)         4.203125       3.809174     0.8914069       2.140616
>     Omega(edhec[,13],method="interp",output="point")
Error in FUN(newX[, i], ...) : 
  requireNamespace("Hmisc", quietly = TRUE) is not TRUE
Calls: Omega -> apply -> FUN -> stopifnot
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
ES  8.013  0.029  11.409
MCA 3.651  0.049   5.223
Found the following HTML validation problems:
Return.Geltner.html:58:32 (Return.Geltner.Rd:27): Warning: trimming empty <code>
centeredmoments.html:24:32 (centeredmoments.Rd:37): Warning: trimming empty <code>
Packages required but not available: 'ggplot2', 'tidyr', 'dplyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFactor', 'bayesplot', 'blavaan', 'brms', 'car',
  'cplm', 'DHARMa', 'forecast', 'ftExtra', 'gamm4', 'ggplot2',
  'glmmTMB', 'Hmisc', 'ivreg', 'lme4', 'loo', 'mlogit', 'nestedLogit',
  'patchwork', 'qqplotr', 'rempsyc', 'rstanarm', 'see', '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: 'Hmisc', 'rms'

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:
  'colourpicker', 'ggplot2', 'testthat'

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

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

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

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
  > 
  > testthat::test_check("permChacko")
  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
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', 'dabestr', '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
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) jackal.Rd:32: Escaped LaTeX specials: \&
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## Test `permute` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'buildmer', 'car', 'ggplot2', 'glmmTMB', 'lme4', 'viridis'
Running examples in ‘permutes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterperm.glm
> ### Title: Cluster-based permutation tests for time series data, based on
> ###   generalized linear models or other 'buildmer' models. This is an
> ###   alias for 'clusterperm.lm' provided for discoverability.
> ### Aliases: clusterperm.glm
> 
> ### ** Examples
> 
> ## Don't show: 
> perms <- clusterperm.glm(Fz ~ Deviant * Session,data=MMN[MMN$Time > 200 & MMN$Time < 205,],series.var=~Time,nperm=2)
Error in loadNamespace(x) : there is no package called ‘buildmer’
Calls: clusterperm.glm ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘buildmer.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'ggplot2''
Failed with error:  'there is no package called 'viridis''

Quitting from lines 62-63 [permplot] (buildmer.Rmd)
Error: processing vignette 'buildmer.Rmd' failed with diagnostics:
Please install the following missing packages: ggplot2, Please install the following missing packages: viridis
--- failed re-building ‘buildmer.Rmd’

--- re-building ‘permutes.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'ggplot2''
Failed with error:  'there is no package called 'viridis''

Quitting from lines 69-70 [permplot] (permutes.Rmd)
Error: processing vignette 'permutes.Rmd' failed with diagnostics:
Please install the following missing packages: ggplot2, Please install the following missing packages: viridis
--- failed re-building ‘permutes.Rmd’

SUMMARY: processing the following files failed:
  ‘buildmer.Rmd’ ‘permutes.Rmd’

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

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

Package suggested but not available for checking: ‘perryExamples’

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', 'roxygen2'

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: ‘personalized’

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.
Packages required but not available: 'devtools', 'purrr', 'usethis'

Packages suggested but not available for checking: 'dplyr', '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: ‘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: 'igraph', '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/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', 'purrr'
'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: 'readxl', 'stringr', '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', 'readr', 'RSQLite', 'tidyr'

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:
  'Hmisc', 'dplyr', 'ggplot2', 'stringr', 'reshape2', 'tidyselect'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AICcmodavg', 'BTSPAS', 'ggplot2', 'reshape2', 'SPAS', 'stringr',
  '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 suggested but not available for checking:
  'lubridate', 'testthat', 'dplyr'
'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', 'DiagrammeR', 'purrr'

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

Package suggested but not available for checking: ‘lme4’

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:
  'devtools', 'ggplot2', 'stringr', 'kableExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) DTV.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
'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: 'igraph', 'ggplot2'

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

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

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

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

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

Package suggested but not available for checking: ‘gsDesign’

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

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', 'stringr', 'factoextra', 'bipartite'

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

Package suggested but not available for checking: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'purrr', 'huxtable'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'readr', 'gt', 'readxl', 'kableExtra',
  'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'diffdf', 'pkgdown', 'roxygen2', 'testthat', 'tibble',
  'usethis', 'metacore', 'metatools'
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:
  > # 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:
  'devtools', 'pkgdown', 'testthat', 'roxygen2', 'usethis'
Package required but not available: ‘altair’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'reshape2', 'dplyr', '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.
Packages required but not available:
  'lubridate', 'plotly', 'zeitgebr', 'shinyFiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) phasePlaneAnalysis.Rd:84: Lost braces; missing escapes or markup?
    84 | identified {see (3) above}, if this point is a saddle then the manifolds are
       |            ^
Running ‘testthat.R’ [0s/1s]
Running 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: ‘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: ‘ggplot2’

Package suggested but not available for checking: ‘cowplot’

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.
Found the following files/directories:
  ‘test.pdf’
Packages required but not available:
  'adabag', 'C50', 'caret', 'dplyr', 'kknn', 'klaR', 'themis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'randomForestSRC'
Packages required but not available: 'dplyr', 'plotly', 'purrr', 'readr'

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:
  'broom', 'dplyr', 'purrr', 'tibble', 'tidyselect', 'tidyr'

Packages suggested but not available for checking: 'readxl', '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', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘daymetr’

Packages suggested but not available for checking: 'testthat', 'plotly'

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', 'stringr', 'lubridate', 'ggplot2', '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: ‘purrr’

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'HelpersMG'

Packages suggested but not available for checking: 'progress', 'car'

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.
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: 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
Packages required but not available: 'lme4', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Hmisc', 'cowplot', 'ggplot2', 'reshape2', '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: ‘lubridate’

Packages suggested but not available for checking:
  'dplyr', 'geomtextpath', 'ggplot2', 'testthat', 'tidyterra'

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', 'lme4', 'purrr', 'tidyr', '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: ‘car’

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘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 HTML validation problems:
estimate.probability.html:33:1 (estimate.probability.Rd:25): Warning: trimming empty <li>
estimate.probability.html:35:1 (estimate.probability.Rd:26): Warning: trimming empty <li>
Package required but not available: ‘purrr’

Packages suggested but not available for checking:
  'lubridate', 'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'coxphf', 'nph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘smallstuff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'blme', 'tibble', 'FactoMineR', 'factoextra', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'qwraps2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘phoenix.Rmd’ using rmarkdown

Quitting from lines 17-29 [setup] (phoenix.Rmd)
Error: processing vignette 'phoenix.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building ‘phoenix.Rmd’

SUMMARY: processing the following file failed:
  ‘phoenix.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: ‘readr’

Packages suggested but not available for checking:
  'tidyr', 'dplyr', 'testthat', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'devtools'
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: ‘photobiology’

Packages suggested but not available for checking:
  'ggplot2', 'ggspectra', 'photobiologyWavebands'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'photobiology', 'stringr', 'lubridate', 'tibble', 'dplyr', 'tidyr',
  'tidyselect', 'readr', 'readxl'

Packages suggested but not available for checking:
  'hyperSpec', 'pavo', 'fda.usc', 'ggplot2', 'ggspectra',
  'photobiologyWavebands', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  'ggspectra', 'photobiologyWavebands', 'ggplot2', 'photobiologyLEDs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  'photobiologyWavebands', 'photobiologyLamps', 'ggspectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'photobiology', 'photobiologyWavebands'

Packages suggested but not available for checking: 'ggplot2', 'ggspectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'stringr', 'lubridate', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'lutz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  'photobiologyWavebands', 'ggspectra', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  'photobiologyWavebands', 'ggspectra', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'furrr', 'gunit', 'progress', 'purrr', 'readr',
  'stringr', 'tealeaves'

Packages suggested but not available for checking:
  'brms', 'broom', 'testthat', 'tibble', 'tidyr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'readr', 'stringr', 'tibble'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) 11_d.init.method.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:27-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:29: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘phylobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'forcats', 'ggnewscale', 'ggplot2', 'ggraph',
  'igraph', 'tidygraph', 'vctrs'

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: ‘gdistance’
Error(s) in re-building vignettes:
  ...
--- re-building ‘phylin_tutorial.Snw’ using Sweave
--- finished re-building ‘phylin_tutorial.Snw’

--- re-building ‘resistance_tutorial.Snw’ using Sweave

Error: processing vignette 'resistance_tutorial.Snw' failed with diagnostics:
 chunk 7 (label = conductanceraster) 
Error in library(gdistance) : there is no package called ‘gdistance’

--- failed re-building ‘resistance_tutorial.Snw’

SUMMARY: processing the following file failed:
  ‘resistance_tutorial.Snw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rncl', 'RNeXML'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phylobase’

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 suggested but not available for checking:
  'phytools', 'testthat', 'TreeSim'
Note: skipping ‘tutorial.Rmd’ due to unavailable dependencies: 'TreeSim'
Packages suggested but not available for checking: 'dendextend', '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
Error(s) in re-building vignettes:
  ...
--- re-building ‘phylogram-vignette.Rmd’ using rmarkdown
** Processing: figures/unnamed-chunk-3-1.png
1500x750 pixels, 8 bits/pixel, 244 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8281 bytes
Input file size = 9115 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 5929
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 4704
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 4704

Output IDAT size = 4704 bytes (3577 bytes decrease)
Output file size = 4782 bytes (4333 bytes = 47.54% decrease)


Quitting from lines 223-243 [unnamed-chunk-5] (phylogram-vignette.Rmd)
Error: processing vignette 'phylogram-vignette.Rmd' failed with diagnostics:
there is no package called 'dendextend'
--- failed re-building ‘phylogram-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘phylogram-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
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:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggm', 'ggplot2', 'ggraph', 'igraph', 'purrr', '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: 'phylobase', '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 ‘phyloraster-vignette.Rmd’ using rmarkdown

Quitting from lines 89-94 [unnamed-chunk-3] (phyloraster-vignette.Rmd)
Error: processing vignette 'phyloraster-vignette.Rmd' failed with diagnostics:
there is no package called 'phylobase'
--- failed re-building ‘phyloraster-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘phyloraster-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'phangorn', 'igraph', 'clustMixType'

Package suggested but not available for checking: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'purrr', 'reshape2', 'testthat'
Running examples in ‘phylosamp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gendist_roc_format
> ### Title: Make ROC curve from sensitivity and specificity
> ### Aliases: gendist_roc_format
> 
> ### ** Examples
> 
> # ebola-like pathogen
> R <- 1.5
> mut_rate <- 1
> 
> # use simulated generation distributions
> data('genDistSim')
> mean_gens_pdf <- as.numeric(genDistSim[genDistSim$R == R, -(1:2)])
> 
> # get theoretical genetic distance dist based on mutation rate and generation parameters
> dists <- as.data.frame(gendist_distribution(mut_rate = mut_rate,
+                        mean_gens_pdf = mean_gens_pdf,
+                        max_link_gens = 1))
> 
> dists <- reshape2::melt(dists,
+                         id.vars = 'dist',
+                         variable.name = 'status',
+                         value.name = 'prob')
Error in loadNamespace(x) : there is no package called ‘reshape2’
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 ‘L1_FalseDiscoveryRate.Rmd’ using rmarkdown
--- finished re-building ‘L1_FalseDiscoveryRate.Rmd’

--- re-building ‘L2_SampleSize.Rmd’ using rmarkdown
--- finished re-building ‘L2_SampleSize.Rmd’

--- re-building ‘L3_SensitivitySpecificity.Rmd’ using rmarkdown
--- finished re-building ‘L3_SensitivitySpecificity.Rmd’

--- re-building ‘L4_IllustrativeExamples.Rmd’ using rmarkdown

Quitting from lines 15-19 [setup] (L4_IllustrativeExamples.Rmd)
Error: processing vignette 'L4_IllustrativeExamples.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘L4_IllustrativeExamples.Rmd’

--- re-building ‘V1_CoefficientDetectionBias.Rmd’ using rmarkdown
--- finished re-building ‘V1_CoefficientDetectionBias.Rmd’

--- re-building ‘V2_SampleSizeCrossSectional.Rmd’ using rmarkdown
--- finished re-building ‘V2_SampleSizeCrossSectional.Rmd’

--- re-building ‘V3_ProbCrossSectional.Rmd’ using rmarkdown
--- finished re-building ‘V3_ProbCrossSectional.Rmd’

--- re-building ‘V4_SampleSizePeriodic.Rmd’ using rmarkdown
--- finished re-building ‘V4_SampleSizePeriodic.Rmd’

--- re-building ‘V5_ProbDetectPeriodic.Rmd’ using rmarkdown
--- finished re-building ‘V5_ProbDetectPeriodic.Rmd’

--- re-building ‘V6_IllustrativeExample.Rmd’ using rmarkdown
--- finished re-building ‘V6_IllustrativeExample.Rmd’

SUMMARY: processing the following file failed:
  ‘L4_IllustrativeExamples.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'sem', 'phylobase', 'phylopath'

Packages suggested but not available for checking:
  'semPlot', 'Rphylopars', 'phyr', 'ggplot2', 'testthat',
  'phylosignal', 'adephylo'

Packages which this enhances but not available for checking:
  'phytools', 'DiagrammeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'phyloseq', 'ggnetwork', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'adephylo', 'igraph', 'phylobase'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'NHPoisson', 'phylobase'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lme4', 'nloptr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'pez', 'INLA', 'logistf', 'ggplot2', 'ggridges',
  'DHARMa', 'rr2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RSQLite', 'keras', 'rms'
checkRd: (-1) pa-internal.Rd:11: Lost braces
    11 | code{l2df}: convert list to data.frame
       |     ^
checkRd: (-1) pa-internal.Rd:14: Lost braces
    14 | code{convertTZ}: force a new timezone on datetime
       |     ^
checkRd: (-1) pa-internal.Rd:16: Lost braces
    16 | code{createTime}: create datetime variable
       |     ^
checkRd: (-1) pa-internal.Rd:18: Lost braces
    18 | code{addDayIndex}: create ID_day variable from timestamp
       |     ^
Running examples in ‘PhysicalActivity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deliveryPred
> ### Title: Wrapper Function for Accelerometry data Preprocessing, Feature
> ###   Extraction, and Delivery Prediction
> ### Aliases: deliveryPred
> 
> ### ** Examples
> 
> data(deliveryData)
> 
> predictions <- deliveryPred(df = deliveryData, model = "GLM")
Warning in deliveryPreprocess(df = df) :
  .id unspecified - dummy ID created
Error: deliveryPrediction requires the rms package, please install it.
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
dataCollapser            7.794  0.043  15.401
PhysicalActivity-package 4.135  0.075   8.197
Packages suggested but not available for checking:
  'childsds', 'dplyr', 'ggplot2', 'testthat', 'tidyr'
Running ‘spelling.R’ [0s/1s]
  Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(physiology)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Everest.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/physiology.Rcheck/vign_test/physiology/vignettes/Everest_files/figure-html/plotres-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31093 bytes
Input file size = 31207 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26847
  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 = 26847

Output IDAT size = 26847 bytes (4246 bytes decrease)
Output file size = 26925 bytes (4282 bytes = 13.72% decrease)

--- finished re-building ‘Everest.Rmd’

--- re-building ‘IdealWeightComparison.Rmd’ using rmarkdown

Quitting from lines 16-43 [unnamed-chunk-1] (IdealWeightComparison.Rmd)
Error: processing vignette 'IdealWeightComparison.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘IdealWeightComparison.Rmd’

--- re-building ‘NeonatalVentilation.Rmd’ using rmarkdown

Quitting from lines 21-31 [calc] (NeonatalVentilation.Rmd)
Error: processing vignette 'NeonatalVentilation.Rmd' failed with diagnostics:
there is no package called 'childsds'
--- failed re-building ‘NeonatalVentilation.Rmd’

SUMMARY: processing the following files failed:
  ‘IdealWeightComparison.Rmd’ ‘NeonatalVentilation.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bestNormalize', 'dplyr', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phangorn’

Packages suggested but not available for checking: 'animation', 'geiger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 ‘test-making-price-indexes.R’ [0s/1s]
  Comparing ‘test-making-price-indexes.Rout’ to ‘test-making-price-indexes.Rout.save’ ... OK
  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
checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Specified C++11: please drop specification unless essential
Packages required but not available: 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'dplyr'
Running examples in ‘picR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PIC.mlm
> ### Title: PIC method for Multivariable Linear Models
> ### Aliases: PIC.mlm
> 
> ### ** Examples
> 
> require(dplyr, quietly = TRUE)
> data(iris)
> 
> # Fit a bivariable regression model
> mod <- lm(cbind(Sepal.Length, Sepal.Width) ~ ., data = iris)
> class(mod)
[1] "mlm" "lm" 
> 
> # Hypothetical validation data
> set.seed(1)
> vdat <- iris[sample(1:nrow(iris), 10),]
> 
> # tPIC, completely unobserved response data
> PIC(object = mod, newdata = vdat %>% dplyr::mutate(Sepal.Length = NA, Sepal.Width = NA))
Error in vdat %>% dplyr::mutate(Sepal.Length = NA, Sepal.Width = NA) : 
  could not find function "%>%"
Calls: PIC -> PIC.mlm
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', 'FrF2', 'FrF2.catlg128'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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.
Packages required but not available: 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'animation', 'ggplot2', 'magick', 'rayrender', 'rayvertex',
  'testthat', 'tweenr', 'vdiffr', 'xmpdf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'DiagrammeR', 'igraph', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'ggforce', 'forcats'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gh', 'lubridate'

Packages suggested but not available for checking: 'readr', 'testthat'

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: ‘vctrs’

Packages suggested but not available for checking:
  'DiagrammeR', 'dplyr', 'ggplot2', 'lubridate', 'nycflights13',
  'testthat', 'tibble', '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.
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', 'stringr', 'tibble', 'tidyselect', 'lubridate', 'plotly',
  'reshape2'

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/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: ‘tibble’

Packages suggested but not available for checking:
  'tidyverse', 'pinnacle.API', 'Lahman'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'lubridate', 'tidyverse', 'testthat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘pinochet.Rmd’ using rmarkdown

Quitting from lines 52-58 [table] (pinochet.Rmd)
Error: processing vignette 'pinochet.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘pinochet.Rmd’

SUMMARY: processing the following file failed:
  ‘pinochet.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) pinp.Rd:60: Lost braces; missing escapes or markup?
    60 |   {current date}"}
       |   ^
Packages required but not available: 'purrr', 'tibble'

Packages suggested but not available for checking:
  'archive', 'arrow', 'AzureStor', 'googledrive', 'Microsoft365R',
  'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nloptr', 'furrr', 'dplyr'

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: ‘ggplot2’

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 suggested but not available for checking:
  'testthat', 'modelr', 'tidyverse'
'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 ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 119-141 [unnamed-chunk-9] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- 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:
  > 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.
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++11: please drop specification unless essential
'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: 'rstan', 'bayesplot'

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: ‘httptest’
Running ‘spelling.R’ [0s/1s]
  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 ‘pivotaltrackR.Rmd’ using rmarkdown

Quitting from lines 12-15 [unnamed-chunk-1] (pivotaltrackR.Rmd)
Error: processing vignette 'pivotaltrackR.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘pivotaltrackR.Rmd’

SUMMARY: processing the following file failed:
  ‘pivotaltrackR.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'purrr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tibble'

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', 'lubridate', 'basictabler', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tibble', 'purrr', 'lubridate', 'dplyr', 'stringr', 'readr', '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: ‘tibble’

Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggbeeswarm', 'ggplot2', 'ggrepel', '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:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'beepr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) get_pixels.Rd:27-29: Lost braces
    27 | if (interactive()) {
       |                    ^
'LazyData' is specified without a 'data' directory
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 required but not available: 'broom', 'reshape2'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lubridate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mockery', 'testthat'
Running ‘build-tools.R’ [1s/2s]
  Running ‘testthat.R’ [0s/1s]
Running 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:
  'mockery', 'pillar', '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: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'asciicast', 'mockery', 'testthat', 'tibble'
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'downlit', 'purrr', 'tibble'

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 required but not available:
  'ggnetwork', 'ggplot2', 'dplyr', 'igraph', 'intergraph', 'networkD3',
  'network', 'tibble'

Package suggested but not available for checking: ‘sna’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DiagrammeR', 'dplyr', '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: ‘roxygen2’
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 ‘wipe.R’ [2s/2s]
Running 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:
  'devtools', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'igraph', 'ggplot2', 'ggrepel', 'testthat', 'cowplot'
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: ‘igraph’

Packages suggested but not available for checking:
  'ggplot2', 'pkgdown', '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:
  'mockery', 'pillar', '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: 'devtools', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘PKI/libs/PKI.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 required but not available: 'dplyr', 'purrr', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'pmxTools', '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', 'mockery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'httk', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'readr', 'dplyr'

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', 'kableExtra'
Running examples in ‘placer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plastic.ci
> ### Title: Confidence intervals of plastic prevalence probability
> ### Aliases: plastic.ci
> 
> ### ** Examples
> 
> plastic.ci(rbinom(1000,1,0.5), 30, 100)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: plastic.ci ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PlAcER.Rmd’ using rmarkdown

Quitting from lines 52-57 [unnamed-chunk-1] (PlAcER.Rmd)
Error: processing vignette 'PlAcER.Rmd' failed with diagnostics:
could not find function "%>%"
--- failed re-building ‘PlAcER.Rmd’

SUMMARY: processing the following file failed:
  ‘PlAcER.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'BayesMallows', 'BradleyTerry2', 'PLMIX', 'StatRank', 'kableExtra',
  '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: ‘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: 'caret', 'lubridate', 'MESS', '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', 'tidyr', 'lubridate'

Packages suggested but not available for checking:
  'highcharter', 'reactablefmtr', 'tidyverse', 'DiagrammeR',
  'networkD3', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'httr2', 'purrr', 'readr', 'stringr', 'tibble', '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: ‘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', '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:
  > # 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: ‘igraph’

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', 'VariantAnnotation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'VariantAnnotation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plsRcox’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggdendro', 'ggplot2', 'plotly', 'reshape2', '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: ‘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: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
checkRd: (-1) one_design.Rd:125-126: Lost braces
   125 | function serves for the purpose of spot-testing for any pre-specified {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
Error(s) in re-building vignettes:
  ...
--- re-building ‘PlatformDesign.Rmd’ using rmarkdown

Quitting from lines 20-22 [setup] (PlatformDesign.Rmd)
Error: processing vignette 'PlatformDesign.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘PlatformDesign.Rmd’

SUMMARY: processing the following file failed:
  ‘PlatformDesign.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', '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
Error(s) in re-building vignettes:
  ...
--- re-building ‘testing-platowork.Rmd’ using rmarkdown

Quitting from lines 59-75 [data] (testing-platowork.Rmd)
Error: processing vignette 'testing-platowork.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘testing-platowork.Rmd’

SUMMARY: processing the following file failed:
  ‘testing-platowork.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.
Packages required but not available: 'dplyr', 'ggplot2', 'ggtext', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'purrr', 'stringr', 'tibble', 'tidyr',
  'worldfootballR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'mlogit', 'dfidx'

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', 'keras', 'ggraph', '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: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mapedit’
To use viewer = 'mapview', first install the required packages:mapedit

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Found the following HTML validation problems:
efourier_power.html:100:1 (efourier_power.Rd:35): Warning: trimming empty <li>
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', 'ggforce', 'ggrepel', 'cowplot', 'UpSetR', 'dplyr',
  'igraph'

Packages suggested but not available for checking: 'testthat', 'mockery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'optimx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggmcmc', 'reshape2', 'rankdist', 'StatRank',
  'PlackettLuce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'AER', 'car'
Error(s) in re-building vignettes:
  ...
--- re-building ‘A_plmPackage.Rmd’ using rmarkdown

Quitting from lines 2057-2059 [car-vcovHC] (A_plmPackage.Rmd)
Error: processing vignette 'A_plmPackage.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building ‘A_plmPackage.Rmd’

--- re-building ‘B_plmFunction.Rmd’ using rmarkdown
--- finished re-building ‘B_plmFunction.Rmd’

--- re-building ‘C_plmModelComponents.Rmd’ using rmarkdown

Quitting from lines 179-180 [unnamed-chunk-11] (C_plmModelComponents.Rmd)
Error: processing vignette 'C_plmModelComponents.Rmd' failed with diagnostics:
there is no package called 'AER'
--- failed re-building ‘C_plmModelComponents.Rmd’

SUMMARY: processing the following files failed:
  ‘A_plmPackage.Rmd’ ‘C_plmModelComponents.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'nloptr', 'igraph', 'dplyr', 'tidyr', 'purrr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'usethis', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) delta2a.Rd:21: Lost braces; missing escapes or markup?
    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
checkRd: (-1) ordprob.mple.Rd:29: Lost braces
    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
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', 'reshape2', 'pcutils', 'ggforce', 'magick'

Package suggested but not available for checking: ‘geomtextpath’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'ggdendro'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'aplot', 'dplyr', 'ggplotify'
Error(s) in re-building vignettes:
  ...
--- re-building ‘plotbb.Rmd’ using rmarkdown

Quitting from lines 21-26 [style] (plotbb.Rmd)
Error: processing vignette 'plotbb.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘plotbb.Rmd’

SUMMARY: processing the following file failed:
  ‘plotbb.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plotly’

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'gganimate', 'ggnewscale', 'ggplot2', 'lubridate',
  'rerddap', 'tidyr', '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', 'plotly', 'purrr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) add_bars.Rd:15: Lost braces
    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |       ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'mixtools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggfittext', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘compare_depmixS4.Rmd’ using knitr
** Processing: figure/unnamed-chunk-2-1.png
504x504 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 29807 bytes
Input file size = 30701 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 28437
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 28000
  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 = 28000

Output IDAT size = 28000 bytes (1807 bytes decrease)
Output file size = 28078 bytes (2623 bytes = 8.54% decrease)


Quitting from lines 89-113 [unnamed-chunk-5] (compare_depmixS4.Rmd)
Error: processing vignette 'compare_depmixS4.Rmd' failed with diagnostics:
object 'nb.dt' not found
--- failed re-building ‘compare_depmixS4.Rmd’

--- re-building ‘multiple_sequences.Rmd’ using knitr

Quitting from lines 18-34 [unnamed-chunk-1] (multiple_sequences.Rmd)
Error: processing vignette 'multiple_sequences.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘multiple_sequences.Rmd’

SUMMARY: processing the following files failed:
  ‘compare_depmixS4.Rmd’ ‘multiple_sequences.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Hmisc', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'gapminder'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’

Package which this enhances but not available for checking: ‘plotly’
'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:
  'ggplot2', 'tidyr', 'dplyr', 'vctrs', 'tibble', 'purrr'

Packages suggested but not available for checking:
  'ggthemes', 'GGally', 'ggalluvial', 'testthat', 'shinytest', 'broom',
  'dendextend', 'IRdisplay', 'forcats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
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:
  'mixtools', 'testthat', 'dplyr', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'C50', 'mlr', 'pre'
Packages required but not available: 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein-package.Rd:20: Lost braces
    20 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'stringr'

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: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘EnvStats’

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: ‘FactoMineR’
Package required but not available: ‘reshape2’

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: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'parsnip', 'dplyr', 'mixOmics', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'modeldata', '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: 'kableExtra', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'FactoMineR', '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 ‘plspm_introduction.Rnw’ using knitr

Quitting from lines 308-327 [rus_pls_xloads_ggplot] (plspm_introduction.Rnw)
Error: processing vignette 'plspm_introduction.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘plspm_introduction.Rnw’

SUMMARY: processing the following file failed:
  ‘plspm_introduction.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plsRglm’

Package suggested but not available for checking: ‘bipartite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test_import.R’ [0s/1s]
  Running ‘test_library.R’ [5s/10s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'plsRglm', 'mixOmics', 'survAUC', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bipartite', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘progress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'coreSim', '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 suggested but not available for checking:
  'testthat', 'readr', 'arrow', 'mockery'
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 ‘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 ‘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:
  'dplyr', 'purrr', 'readr', 'stringr', 'tibble', 'tidyr',
  'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'gt', 'testthat', 'waldo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) plu_more.Rd:16: Lost braces; missing escapes or markup?
    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
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:
  'baizer', 'dplyr', 'ggh4x', 'ggplot2', 'ggsci', 'purrr', 'repr',
  'stringr', 'tibble', 'tidyr'

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: ‘tableone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clusterProfiler', 'org.Hs.eg.db', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'stringr', 'tidyr', 'patchwork'

Packages suggested but not available for checking:
  'DESeq2', 'plotly', 'testthat', 'trelliscopejs', 'pmartRdata',
  'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'ggplot2', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'NSM3'
checkRd: (-1) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available:
  'dplyr', 'geiger', 'ggplot2', 'tidyr', 'phytools'

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', 'enviGCMS'

Package suggested but not available for checking: ‘MSnbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'tidyr', 'stringr'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'caret', 'forecast', 'rattle', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'pmml'
Running examples in ‘pmmlTransformations-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DiscretizeXform
> ### Title: Discretizes a continuous variable to a discrete one as indicated
> ###   by interval mappings. This is in accordance to the PMML element:
> ###   *Discretize*
> ### Aliases: DiscretizeXform
> ### Keywords: manip
> 
> ### ** Examples
> 
> # Load the pmmlTransformations package
>     library(pmmlTransformations)
>     library(pmml)
Error in library(pmml) : there is no package called ‘pmml’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘FunctionXform.Rmd’ using rmarkdown

Quitting from lines 31-34 [unnamed-chunk-2] (FunctionXform.Rmd)
Error: processing vignette 'FunctionXform.Rmd' failed with diagnostics:
there is no package called 'pmml'
--- failed re-building ‘FunctionXform.Rmd’

SUMMARY: processing the following file failed:
  ‘FunctionXform.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'bigrquery', 'RMariaDB', 'RPostgres', 'RSQLite', '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) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
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:
  'dplyr', 'pillar', 'readr', 'shinyFiles', '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/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:
  'patchwork', 'ggplot2', 'dplyr', 'tibble', 'gghalves', 'ggdist',
  'stringr', 'PKNCA'

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', 'projmgr', 'readr', 'readxl', 'tibble'

Packages suggested but not available for checking: 'SIPDIBGE', 'srvyr'

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.
Packages required but not available:
  'dplyr', 'projmgr', 'readr', 'readxl', 'tibble'

Packages suggested but not available for checking: 'SIPDIBGE', 'srvyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'projmgr', 'readr', 'readxl', 'tibble'

Packages suggested but not available for checking: 'SIPDIBGE', 'srvyr'

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
Packages required but not available: 'dplyr', 'tibble', 'nloptr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'purrr', 'tibble', 'dplyr', 'usethis'

Packages suggested but not available for checking:
  'testthat', 'mockery', 'httptest', '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'

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', 'fuzzyjoin', 'progress', 'purrr', 'readr', '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
Packages required but not available: 'ggplot2', 'logistf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'SmarterPoland'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'blastula', 'dplyr', 'dbplyr', 'gt', 'testthat', 'tibble', 'tidyr',
  'tidyselect'

Packages suggested but not available for checking:
  'arrow', 'bigrquery', 'ggforce', 'ggplot2', 'lubridate', 'RSQLite',
  'RPostgres', 'readr', 'sparklyr', 'odbc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'inlabru', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'INLA', 'ggmap', 'ggpolypath', 'cowplot', 'kableExtra',
  'spocc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'ggplot2', '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:
  'ggplot2', 'dplR', 'TripleR', 'DescTools'

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’
checkRd: (-1) pois.fe.robust.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'parsnip', 'dplyr', '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: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Packages required but not available: 'dplyr', 'ggplot2', 'reshape2'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'DiagrammeR'
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', 'tidyverse', 'car', 'purrr', 'rstatix', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'weights', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'automagic', '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: '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: 'robotstxt', 'rvest', 'usethis'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'purrr', 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘targeted’

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: ‘brms’

Packages suggested but not available for checking:
  'rstan', 'pollimetrydata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'tidyr', 'labelled', 'forcats'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'tidytext', 'igraph'
Running ‘testthat.R’ [0s/1s]
Running 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', '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: ‘qspray’

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 ‘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: 'igraph', 'MDSMap'

Packages suggested but not available for checking:
  'ggplot2', 'Hmisc', 'reshape2', 'updog', 'mappoly'

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) inputData.Rd:94: Lost braces
    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) inputData.Rd:95: Lost braces
    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) preprocessData.Rd:81: Lost braces
    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) preprocessData.Rd:82: Lost braces
    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
Packages required but not available: 'lubridate', '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: 'tibble', 'reshape2', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'reshape2'

Packages suggested but not available for checking:
  'igraph', 'mappoly', 'polymapR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'VariantAnnotation', 'GenomicFeatures', 'ggplot2', 'adegenet'
Packages unavailable to check Rd xrefs: ‘GenomicFeatures’, ‘VariantAnnotation’
Package suggested but not available for checking: ‘adegenet’
checkRd: (-1) calculateDIC.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateDIC.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polySegratioMM-package.Rd:70-72: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'purrr', 'furrr', 'stringr', 'tidyr', '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', 'tidyr', 'ggplot2', '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: ‘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: ‘pomdp’
Packages required but not available: 'tibble', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'qgraph'

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: 'bayesplot', 'ggplot2'
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr', 'nloptr'
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 required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tibble', '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 ‘Intro_PoolDilutionR.Rmd’ using rmarkdown

Quitting from lines 114-126 [Multi-sample Example Input] (Intro_PoolDilutionR.Rmd)
Error: processing vignette 'Intro_PoolDilutionR.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘Intro_PoolDilutionR.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_PoolDilutionR.Rmd’

Error: Vignette re-building failed.
Execution halted
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
Packages required but not available: 'DiagrammeR', 'progress'

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:
  > # 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 ‘poolvignette.Rmd’ using rmarkdown
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'number of pools'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.


Quitting from lines 47-67 [number of pools] (poolvignette.Rmd)
Error: processing vignette 'poolvignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘poolvignette.Rmd’

SUMMARY: processing the following file failed:
  ‘poolvignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'dvmisc', 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dbplyr', 'dplyr', 'RSQLite', 'testthat', 'tibble'
Running examples in ‘pool-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DBI-wrap
> ### Title: DBI methods (simple wrappers)
> ### Aliases: DBI-wrap dbDataType,Pool-method dbGetQuery,Pool,ANY-method
> ###   dbExecute,Pool,ANY-method dbListFields,Pool,ANY-method
> ###   dbListTables,Pool-method dbListObjects,Pool-method
> ###   dbReadTable,Pool,ANY-method dbWriteTable,Pool,ANY-method
> ###   dbCreateTable,Pool-method dbAppendTable,Pool-method
> ###   dbExistsTable,Pool,ANY-method dbRemoveTable,Pool,ANY-method
> ###   dbIsReadOnly,Pool-method sqlData,Pool-method
> ###   sqlCreateTable,Pool-method sqlAppendTable,Pool-method
> ###   sqlInterpolate,Pool-method sqlParseVariables,Pool-method
> ###   dbQuoteIdentifier,Pool,ANY-method dbUnquoteIdentifier,Pool-method
> ###   dbQuoteLiteral,Pool-method dbQuoteString,Pool,ANY-method
> ###   dbAppendTableArrow,Pool-method dbCreateTableArrow,Pool-method
> ###   dbGetQueryArrow,Pool-method dbReadTableArrow,Pool-method
> ###   dbSendQueryArrow,Pool-method dbWriteTableArrow,Pool-method
> ### Keywords: internal
> 
> ### ** Examples
> 
> mtcars1 <- mtcars[ c(1:16), ] # first half of the mtcars dataset
> mtcars2 <- mtcars[-c(1:16), ] # second half of the mtcars dataset
> 
> pool <- dbPool(RSQLite::SQLite())
Error in loadNamespace(x) : there is no package called ‘RSQLite’
Calls: dbPool ... 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
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.r’ [0s/1s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > ### to also run skip_on_cran() tests, uncomment:
  > #Sys.setenv(NOT_CRAN="true")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'rstan', 'brms', 'lme4', 'stringr', 'progress'

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: ‘roxygen2’
Packages required but not available: 'R2jags', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘magick’
checkRd: (-1) plot.tfam.Rd:17: Lost braces
    17 | objects created using code{tfam_inertia}.}
       |                           ^
checkRd: (-1) popdemo-package.Rd:32: Lost braces
    32 |        code{\link{inertia}} measures asymptotic population density relative to stable
       |            ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |     ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |              ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘popdemo.Rmd’ using rmarkdown

Quitting from lines 94-99 [unnamed-chunk-4] (popdemo.Rmd)
Error: processing vignette 'popdemo.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building ‘popdemo.Rmd’

SUMMARY: processing the following file failed:
  ‘popdemo.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'Hmisc', 'devtools', 'mrgsolve'

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', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR', 'dplyr', 'ggplot2', 'hierfstat', 'poppr',
  'reshape2', 'scatterpie', 'StAMPP', '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:
  'adegenet', 'gap', 'reshape2', 'ggplot2', 'gdistance', 'mmod',
  'GGally'

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: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'ggplot2', 'igraph', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr', 'ggplot2'

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’
Note: skipping ‘burkina-faso-females.Rnw’ due to unavailable dependencies:
  'ggplot2'
Packages required but not available:
  'ggplot2', 'lubridate', 'dplyr', 'tidyr', 'demography', 'forecast',
  'ggpubr', 'DescTools', 'rcompanion', 'corrr', 'Hmisc', 'stringr',
  'rainbow'

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: 'devtools', 'ggplot2', 'roxygen2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'usethis', 'osmdata', 'dplyr'

Packages suggested but not available for checking: 'areal', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rvec', 'tibble', 'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rags2ridges’
Packages required but not available:
  'dplyr', 'forecast', 'timetk', 'lubridate', 'tibble', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forecast', 'lubridate', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'httptest', 'pkgdown', '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 suggested but not available for checking: 'testthat', 'nloptr'
Running examples in ‘PortfolioAnalytics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meucci.ranking
> ### Title: Asset Ranking
> ### Aliases: meucci.ranking
> 
> ### ** Examples
> 
> data(edhec)
> R <- edhec[,1:4]
> p <- rep(1 / nrow(R), nrow(R))
> meucci.ranking(R, p, c(2, 3, 1, 4))
Error in EntropyProg(p, A, b, Aeq, beq) : 
  "package:nloptr" %in% search() || requireNamespace("nloptr",  .... is not TRUE
Calls: meucci.ranking -> EntropyProg -> stopifnot
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'ggfortify', 'readtext', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
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
checkRd: (-1) tradelist-class.Rd:91: 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:
  > # 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', 'dtplyr', 'rugarch', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'ggtext', 'patchwork', '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: ‘rxode2’

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'faux'
Running ‘testthat.R’ [0s/1s]
Running 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', 'testthat', '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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 66-74 [unnamed-chunk-5] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'purrr'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'roxygen2', 'rstan', 'testthat', 'tibble'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > testthat::test_check("PosteriorBootstrap")
  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 ‘PosteriorBootstrap.Rmd’ using rmarkdown_notangle

Quitting from lines 54-61 [unnamed-chunk-1] (PosteriorBootstrap.Rmd)
Error: processing vignette 'PosteriorBootstrap.Rmd' failed with diagnostics:
there is no package called 'rstan'
--- failed re-building ‘PosteriorBootstrap.Rmd’

SUMMARY: processing the following file failed:
  ‘PosteriorBootstrap.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'tibble', 'vctrs', 'pillar', 'distributional'

Packages suggested but not available for checking:
  'testthat', 'caret', 'dplyr', 'tidyr', 'ggplot2', 'ggdist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'refund', 'dplyr', 'tidyr', 'cosinor', 'cosinor2', 'accelerometry',
  'ActCR', 'ActFrag', 'kableExtra', 'GGIR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Packages suggested but not available for checking: 'lme4', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tibble', 'purrr', '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’
'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: 'stringr', 'mcmcse'

Packages suggested but not available for checking:
  'rstan', 'R2jags', 'nimble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘eurostat’
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 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: ‘miscF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'haplo.stats', 'gap', 'ggplot2', 'reshape2', 'BIGDAWG'

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', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'stringr', 'HLMdiag', 'readODS', 'saeRobust',
  'bestNormalize'

Package suggested but not available for checking: ‘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: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'ggplot2', 'ggpubr', 'tidyr', 'FactoMineR', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'reshape2', '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', 'tidyselect', 'vctrs', '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: ‘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', 'bootnet', 'qgraph', 'ggplot2', '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: 'lubridate', 'nasapower'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Packages required but not available: 'dplyr', 'furrr', 'ggplot2', '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', 'weights', 'tourr'

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: ‘factoextra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘fcm.Rmd’ using rmarkdown

Quitting from lines 45-48 [unnamed-chunk-3] (fcm.Rmd)
Error: processing vignette 'fcm.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘fcm.Rmd’

--- re-building ‘upfc.Rmd’ using rmarkdown

Quitting from lines 46-49 [unnamed-chunk-3] (upfc.Rmd)
Error: processing vignette 'upfc.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘upfc.Rmd’

SUMMARY: processing the following files failed:
  ‘fcm.Rmd’ ‘upfc.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'PakPC2017', 'tidyr', 'tmap'

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:
  > # 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', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'GGally', 'ggplot2', 'roxygen2', 'PPtreeViz'

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:
  'animation', 'geiger', 'phangorn', 'phytools'

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', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'stringr', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'genlasso', 'ggplot2', 'cvCovEst'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'censable', 'dplyr', 'readr', 'stringr', 'tibble', 'tidyr'

Package suggested but not available for checking: ‘roxygen2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) ccp_ppm.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
checkRd: (-1) curve_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) gaussian_ppmx.Rd:143: Lost braces; missing escapes or markup?
   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) gaussian_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) ordinal_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) ordinal_ppmx.Rd:147: Lost braces; missing escapes or markup?
   147 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each sujbects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
Packages required but not available: 'ggplot2', 'plotly'

Package suggested but not available for checking: ‘devtools’

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
Package suggested but not available for checking: ‘roxygen2’
Specified C++11: please drop specification unless essential
Packages required but not available:
  'dplyr', 'furrr', 'ggplot2', 'plotly', 'purrr', 'tibble',
  'patchwork', 'tidyr'

Packages suggested but not available for checking:
  'gt', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'ggplot2', 'parsnip'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘progress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DALEX', 'ggplot2', 'dplyr', 'tidyr', 'tibble', 'PPtreeViz',
  'reshape2'

Packages suggested but not available for checking:
  'testthat', 'ggExtra', 'ggparty', 'progress', 'tidyselect',
  'ggforce', 'waterfalls', 'forcats'

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: ‘reshape2’

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) pqrBayes.Rd:58: Lost braces; missing escapes or markup?
    58 | When {sparse=TRUE} (default), spike--and--slab priors are adopted. Otherwise, Laplacian shrinkage will be used.
       |      ^
checkRd: (-1) pqrBayes.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pqrBayes.Rd:63: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Packages required but not available: 'emuR', 'rPraat', 'wrassp'

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', 'Temporal', '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: 'generalCorr', 'ShapleyValue'

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: 'doBy', 'roxygen2'

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:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'precrec'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'tibble', 'purrr', 'forcats'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'roxygen2', 'testthat', 'tidyverse'
Specified C++11: please drop specification unless essential
checkRd: (-1) PRDA.Rd:8: Lost braces; missing escapes or markup?
     8 | Given an hypothetical value of effect size, {PRDA} performs a prospective
       |                                             ^
checkRd: (-1) PRDA.Rd:22: Lost braces; missing escapes or markup?
    22 | In {PRDA} there are two main functions:
       |    ^
checkRd: (-1) PRDA.Rd:51: Lost braces; missing escapes or markup?
    51 | Alternatively, {PRDA} allows users to specify a distribution of plausible
       |                ^
'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 ‘PRDA.Rmd’ using rmarkdown
--- finished re-building ‘PRDA.Rmd’

--- re-building ‘prospective.Rmd’ using rmarkdown
--- finished re-building ‘prospective.Rmd’

--- re-building ‘retrospective.Rmd’ using rmarkdown

Quitting from lines 21-24 [unnamed-chunk-2] (retrospective.Rmd)
Error: processing vignette 'retrospective.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘retrospective.Rmd’

SUMMARY: processing the following file failed:
  ‘retrospective.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'purrr', 'Seurat', 'cowplot', 'patchwork', 'scater', 'ggthemes',
  'dplyr', 'ggplot2', 'DR.SC', 'ggpubr'

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', 'ggpubr', 'lubridate', 'openair'

Packages suggested but not available for checking:
  'kableExtra', 'testthat', 'tibble'

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:
  'ggrepel', '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 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', 'MESS', 'stringr', 'tidyr', 'randomForestSRC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Packages suggested but not available for checking:
  'pkgdown', 'roxygen2', 'styler', 'testthat', 'tibble', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) diagnose_expressions.Rd:39: Lost braces
    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
File ‘precondition/libs/precondition.so’:
  Found non-API calls to R: ‘IS_SCALAR’, ‘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:
  > # 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’

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Packages required but not available:
  'ggplot2', 'dplyr', 'ggiraphExtra', 'modelr', 'purrr', 'stringr',
  'reshape2', 'tidyr'

Package suggested but not available for checking: ‘moonBook’

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', 'MBESS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’

Packages which this enhances but not available for checking:
  'AER', 'caret', 'lme4', 'mlogit', 'sampleSelection'
Running ‘testthat-prediction.R’ [0s/0s]
Running the tests in ‘tests/testthat-prediction.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: ‘tolerance’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'glmmTMB', 'lme4', 'lmerTest', 'car', 'ggplot2', 'pbkrtest', 'plotly'

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:
  'cutpointr', 'dplyr', 'ggplot2', 'tibble', 'tidyr'

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', 'loadeR', 'traineR', 'echarts4r', '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.
Packages required but not available: 'Hmisc', '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', 'lme4'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'ggpubr'

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: 'caret', 'forecast', 'TSPred'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pkgdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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'

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.
Package required but not available: ‘tibble’

Packages suggested but not available for checking: 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', '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’
Error(s) in re-building vignettes:
  ...
--- re-building ‘prepplotOverview.Rmd’ using rmarkdown

Quitting from lines 31-64 [ggplot] (prepplotOverview.Rmd)
Error: processing vignette 'prepplotOverview.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building ‘prepplotOverview.Rmd’

SUMMARY: processing the following file failed:
  ‘prepplotOverview.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.
Packages required but not available: 'RecordLinkage', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'psycho', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'glmertree', 'testthat', 'ggplot2', 'caret', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test_prereg.R’ [0s/1s]
Running the tests in ‘tests/test_prereg.R’ failed.
Complete output:
  > require("testthat")
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_check("prereg")
  Error in test_check("prereg") : could not find function "test_check"
  Execution halted
Packages suggested but not available for checking:
  'googlesheets4', 'haven', 'justifier', 'readxl', 'rvest', 'testthat'
checkRd: (-1) prereg_initialize.Rd:20: Lost braces; missing escapes or markup?
    20 | the (pre)registration form specification (in {preregr} format), see the
       |                                              ^
checkRd: (-1) prereg_initialize.Rd:23: Lost braces; missing escapes or markup?
    23 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
checkRd: (-1) prereg_initialize.Rd:26: Lost braces; missing escapes or markup?
    26 | For an introduction to working with {preregr} (pre)registrations,
       |                                     ^
checkRd: (-1) rmd_templates.Rd:75: Lost braces; missing escapes or markup?
    75 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
checkRd: (-1) rmd_templates.Rd:77: Lost braces; missing escapes or markup?
    77 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
checkRd: (-1) rmd_templates.Rd:81: Lost braces; missing escapes or markup?
    81 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
Running examples in ‘preregr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: source
> ### Title: Programmatically constructing justifier elements
> ### Aliases: source dcsn jstf asrt srce decide decision assert justify
> 
> ### ** Examples
> 
> ### Programmatically create a partial justification object
> exampleAssertion <-
+   preregr::assert(
+     "This is an assertion",
+     source = c(
+       preregr::source('This is a first source'),
+       preregr::source('This is a second source')));
Error in preregr::assert("This is an assertion", source = c(preregr::source("This is a first source"),  : 
  You can't justify without the `justifier` package.
ℹ You can install it with:

install.packages('justifier');
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > testthat::test_check("preregr");
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'dplyr', 'stringr', 'purrr', 'randomcoloR', 'tidyr', 'lubridate',
  'janitor', 'tibble', 'tidyselect', 'framecleaner'

Packages suggested but not available for checking: 'ggplot2', 'badger'

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’

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', 'gt', 'Hmisc', 'shinytest', 'testthat', 'tidyr'
Running ‘presize.R’ [0s/1s]
Running the tests in ‘tests/presize.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 ‘presize.Rmd’ using rmarkdown

Quitting from lines 130-144 [unnamed-chunk-11] (presize.Rmd)
Error: processing vignette 'presize.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘presize.Rmd’

SUMMARY: processing the following file failed:
  ‘presize.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.
Packages required but not available:
  'dplyr', 'gdistance', 'ggmap', 'ggplot2', 'magick', 'readxl',
  '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
Packages suggested but not available for checking: 'testthat', 'vdiffr'
'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: 'mockery', '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', '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
Packages required but not available:
  'broom', 'car', 'dplyr', 'forcats', 'kableExtra', 'plotly',
  'stringr', 'tibble', 'tidycat', 'tidyr', 'tidyselect', 'vip'

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: ‘rosm’
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
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’
'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’

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’

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’

Package suggested but not available for checking: ‘INLA’

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', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'dplyr', 'ggplot2', 'stringr', 'caret', 'strex'

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:
  'dplyr', 'stringr', 'purrr', 'lubridate', '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: ‘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’
'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', 'tidyr'

Packages suggested but not available for checking:
  'bipartite', 'cowplot', 'DiagrammeR', 'igraph', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'reshape2', '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
checkRd: (-1) prim.box.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prim.box.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prim.box.Rd:70: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: '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: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'AER'
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: 'AnnotationDbi', 'org.Hs.eg.db'

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) findbeta.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{lower.v}{logical, if TRUE the specified percentile.value is the upper limit for the mean (or the median or the mode) at the specified confidence level (percentile). If {FALSE} the specified percentile.value is the lower limit for the mean (or the median or the mode) at the specified confidence level (percentile). The default is FALSE.}
       |                                                                                                                                                                               ^
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: 'tidyr', 'dplyr'

Packages suggested but not available for checking:
  'gurobi', 'roxygen2', 'rcbc', 'testthat', 'tmap', 'viridis', 'purrr',
  'readr', 'tibble', '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: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'gurobi', 'rcbc', 'cplexAPI', 'prioritizrdata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'DiagrammeR', 'stringr', 'rio'

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.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DiagrammeR’

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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'dplyr', 'stringr', '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', 'rvest', '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 suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(PRNG)
  
  Attaching package: 'PRNG'
  
  The following objects are masked from 'package:stats':
  
      rcauchy, rexp, rnorm, time
  
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'ggnewscale', 'ggtext', 'dplyr', 'Hmisc', 'ggpattern',
  'DescTools'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'butcher', 'dplyr', 'furrr', 'ggplot2', 'hardhat', 'pillar', 'purrr',
  'tidyr', 'tidyselect', 'tune', 'vctrs', 'workflows', 'yardstick'

Packages suggested but not available for checking:
  'modeldata', 'parsnip', 'recipes', 'rsample', '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', 'rstan'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package 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 required but not available: ‘keras’

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:
  'bupaR', 'processmapR', 'dplyr', 'tidyr', 'DiagrammeR', 'stringr'

Packages suggested but not available for checking:
  'edeaR', 'testthat', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'bupaR', 'edeaR', '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', 'bupaR', 'edeaR', 'DiagrammeR', 'ggplot2', 'stringr',
  'purrr', 'forcats', 'hms', 'plotly', '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', 'dplyr', 'bupaR', 'edeaR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'edeaR', 'dplyr', 'forcats', 'tidyr', 'tidyselect', 'purrr',
  'stringr', 'keras', 'tensorflow', 'ggplot2', 'plotly', 'progress'

Package suggested but not available for checking: ‘lubridate’

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', 'tibble'
Running ‘output.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'
Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'ggplot2'
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: 'fmtr', 'reporter', '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', 'AER'

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
checkRd: (-1) paasche.Rd:91: Lost braces
    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'reshape2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'furrr', 'ggplot2', 'AnnotationDbi', 'DR.SC', 'PRECAST', 'biomaRt',
  'org.Hs.eg.db', 'org.Mm.eg.db', 'Seurat', 'harmony'

Packages suggested but not available for checking: 'scater', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘profile’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
Packages required but not available: 'tibble', 'vctrs'

Packages suggested but not available for checking:
  'dm', 'DiagrammeR', '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’

Packages suggested but not available for checking:
  'tidyverse', 'purrr', 'forcats', 'dplyr', 'ggalluvial', 'ggrepel',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', '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: 'sqldf', 'RSQLite'

Packages suggested but not available for checking:
  'testthat', 'BayesianTools'

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: ‘stringr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) proftools-package.Rd:40: Lost braces
    40 |   by the code{kcachegrind} program available on some operating
       |              ^
Packages required but not available: 'purrr', 'stringr', 'vctrs'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'devtools'

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:
  'igraph', 'patchwork', 'pathwayTMB', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Packages suggested but not available for checking:
  'beepr', 'progress', 'purrr', 'furrr'
Packages required but not available:
  'ggplot2', 'GeneralizedUmatrix', 'plotly'

Packages suggested but not available for checking:
  'DataVisualizations', 'reshape2', 'dendextend', 'DatabionicSwarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'incidence', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'EpiEstim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'readr', 'stringr', 'tibble', 'vctrs'

Packages suggested but not available for checking: 'forcats', '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:
  'feather', 'stringr', 'ggplot2', 'lubridate', 'RSQLite', 'readxl',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gh’

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'purrr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'loo', 'lme4', 'gamm4'

Packages suggested but not available for checking:
  'ggrepel', 'rstanarm', 'brms', 'optimx', 'testthat', 'vdiffr',
  'cmdstanr', 'bayesplot', 'posterior'

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
checkRd: (-1) prolific_prescreener.Rd:254: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_prescreener.Rd:255: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:244: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘rstan’

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.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'purrr', 'testthat', 'vembedr'
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 ‘promises_01_motivation.Rmd’ using rmarkdown
--- finished re-building ‘promises_01_motivation.Rmd’

--- re-building ‘promises_02_intro.Rmd’ using rmarkdown
--- finished re-building ‘promises_02_intro.Rmd’

--- re-building ‘promises_03_overview.Rmd’ using rmarkdown
--- finished re-building ‘promises_03_overview.Rmd’

--- re-building ‘promises_04_futures.Rmd’ using rmarkdown
[WARNING] Div at promises_04_futures.knit.md line 87 column 1 unclosed at promises_04_futures.knit.md line 99 column 1, closing implicitly.
--- finished re-building ‘promises_04_futures.Rmd’

--- re-building ‘promises_05_future_promise.Rmd’ using rmarkdown

Quitting from lines 48-51 [unnamed-chunk-1] (promises_05_future_promise.Rmd)
Error: processing vignette 'promises_05_future_promise.Rmd' failed with diagnostics:
there is no package called 'vembedr'
--- failed re-building ‘promises_05_future_promise.Rmd’

--- re-building ‘promises_06_shiny.Rmd’ using rmarkdown
--- finished re-building ‘promises_06_shiny.Rmd’

--- re-building ‘promises_07_combining.Rmd’ using rmarkdown
--- finished re-building ‘promises_07_combining.Rmd’

--- re-building ‘promises_08_casestudy.Rmd’ using rmarkdown
--- finished re-building ‘promises_08_casestudy.Rmd’

SUMMARY: processing the following file failed:
  ‘promises_05_future_promise.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'reshape2', 'ggplot2', 'ggrepel', 'VIM', 'caret', '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: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'reshape2', 'stringr', 'prophet'

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/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: '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
Package required but not available: ‘tibble’

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', 'ggplot2', 'lubridate', 'rstan', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'readr'

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', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'lubridate'

Packages suggested but not available for checking: 'testthat', 'httptest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cin’
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
  'kableExtra', 'testthat', 'dplyr', 'pkgdown'
checkRd: (-1) computeResponseProbability.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{model}{the item model to use. Accepts \code{grm} or {gpcm}.}
       |                                                           ^
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 ‘PROsetta.Rmd’ using rmarkdown

Quitting from lines 23-27 [unnamed-chunk-1] (PROsetta.Rmd)
Error: processing vignette 'PROsetta.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘PROsetta.Rmd’

SUMMARY: processing the following file failed:
  ‘PROsetta.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
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
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: 'pryr', 'magick', 'dplyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', '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', 'ggplot2', 'ggthemes', 'readr', 'stringr', 'lubridate',
  'narray', 'imputeTS', 'dplyr', 'greybox', 'furrr'

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
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:
  > 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) prototest.univariate.Rd:21: Lost braces
    21 | response variable. Vector of length emph{n}, assumed to be quantitative.
       |                                         ^
Package suggested but not available for checking: ‘AmigaFFH’
Packages suggested but not available for checking:
  'GOSemSim', 'org.Hs.eg.db'
Packages required but not available:
  'dplyr', 'stringr', 'janitor', 'progress', 'purrr', 'tidyr',
  'ggplot2', 'forcats', 'tibble', 'plotly', 'ggrepel', 'readr'

Packages suggested but not available for checking:
  'testthat', 'dendextend', 'heatmaply', 'furrr', 'drc', 'igraph',
  'STRINGdb', 'ggforce'

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:
  > #R
  > library(testthat)   
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'stringr', 'tidyr'

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: ‘provGraphR’

Packages suggested but not available for checking: 'rdt', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'httr2', 'lubridate', 'purrr', 'rvest', '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', '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: ‘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/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: 'rdt', '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: 'rdt', '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: ‘rdt’
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’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > require(proxyC)
  Loading required package: proxyC
  
  Attaching package: 'proxyC'
  
  The following object is masked from 'package:stats':
  
      dist
  
  > 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("proxyC")
  Error in test_check("proxyC") : could not find function "test_check"
  Execution halted
Packages required but not available: 'purrr', 'readr', 'stringr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RSQLite', 'tidyquery', 'sqldf', 'nycflights13', 'dplyr', 'testthat',
  'patrick'
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 ‘knitr.Rmd’ using rmarkdown

Quitting from lines 61-70 [unnamed-chunk-2] (knitr.Rmd)
Error: processing vignette 'knitr.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 ‘knitr.Rmd’

--- re-building ‘prqlr.Rmd’ using rmarkdown

Quitting from lines 64-79 [unnamed-chunk-5] (prqlr.Rmd)
Error: processing vignette 'prqlr.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 ‘prqlr.Rmd’

SUMMARY: processing the following files failed:
  ‘knitr.Rmd’ ‘prqlr.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'liteq', 'RSQLite'

Package suggested but not available for checking: ‘foghorn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Running ‘all_tests.R’ [0s/1s]
Running the tests in ‘tests/all_tests.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRROC.Rnw’ using Sweave

Error: processing vignette 'PRROC.Rnw' failed with diagnostics:
 chunk 47 
Error in library(ggplot2) : there is no package called ‘ggplot2’

--- failed re-building ‘PRROC.Rnw’

SUMMARY: processing the following file failed:
  ‘PRROC.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'bigsnpr', 'bigstatsr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vctrs', 'tibble', 'pillar'

Packages suggested but not available for checking:
  'testthat', 'nycflights13', 'bench'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘geomorph’
Running examples in ‘prWarp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create.pw.be
> ### Title: Principal warps
> ### Aliases: create.pw.be
> 
> ### ** Examples
> 
> # 2D landmark coordinates
> library("geomorph")
Error in library("geomorph") : there is no package called ‘geomorph’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘prWarp-homo-example.Rmd’ using rmarkdown

Quitting from lines 27-33 [data] (prWarp-homo-example.Rmd)
Error: processing vignette 'prWarp-homo-example.Rmd' failed with diagnostics:
there is no package called 'geomorph'
--- failed re-building ‘prWarp-homo-example.Rmd’

--- re-building ‘prWarp-papionin-example.Rmd’ using rmarkdown

Quitting from lines 22-24 [packages] (prWarp-papionin-example.Rmd)
Error: processing vignette 'prWarp-papionin-example.Rmd' failed with diagnostics:
there is no package called 'geomorph'
--- failed re-building ‘prWarp-papionin-example.Rmd’

SUMMARY: processing the following files failed:
  ‘prWarp-homo-example.Rmd’ ‘prWarp-papionin-example.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.
Packages required but not available: 'PogromcyDanych', 'PBImisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggthemes', 'reshape2', 'TriMatch'

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: 'rstan', 'optmatch', 'overlapping'

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', 'GGally', 'riskRegression'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘posterior’

Packages suggested but not available for checking:
  'cmdstanr', 'flexsurv', 'testthat', 'usethis', 'vdiffr', 'tibble',
  'bayesplot', 'WeightIt', 'ggsurvfit', 'ggplot2', 'cobalt', 'gt',
  'gtsummary'

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', 'flexsurv'

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: ‘car’
Running examples in ‘pscl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hurdletest
> ### Title: Testing for the Presence of a Zero Hurdle
> ### Aliases: hurdletest
> ### Keywords: regression
> 
> ### ** Examples
> 
> data("bioChemists", package = "pscl")
> fm <- hurdle(art ~ ., data = bioChemists, dist = "negbin", zero = "negbin")
> hurdletest(fm)
Loading required namespace: car
Failed with error:  ‘there is no package called ‘car’’
Error in hurdletest(fm) : requireNamespace("car") is not TRUE
Calls: hurdletest -> stopifnot
Execution halted
Note: skipping ‘countreg.Rnw’ due to unavailable dependencies: 'car'
Packages required but not available: 'ggplot2', 'reshape2', 'JWileymisc'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DataCombine', 'reshape2', 'rio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) qpc.Rd:43: Lost braces
    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
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:
  'ggplot2', 'reshape2', 'testthat'
checkRd: (-1) riedsid.Rd:92-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riedsid.Rd:94-96: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/0s]
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: 'devtools', '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', 'furrr'

Packages suggested but not available for checking:
  'ggplot2', 'ggspatial', 'purrr', '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: 'ggplot2', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘simulation-study.R’ [2s/3s]
  Running ‘testthat.R’ [0s/1s]
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
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pseval.Rcheck/vign_test/pseval/vignettes/introduction_files/figure-html/plot1-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35717 bytes
Input file size = 35843 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 28075
  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 = 28075

Output IDAT size = 28075 bytes (7642 bytes decrease)
Output file size = 28153 bytes (7690 bytes = 21.45% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pseval.Rcheck/vign_test/pseval/vignettes/introduction_files/figure-html/logrr-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 19264 bytes
Input file size = 20146 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 17116
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 17084
  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 = 17084

Output IDAT size = 17084 bytes (2180 bytes decrease)
Output file size = 17162 bytes (2984 bytes = 14.81% decrease)


Quitting from lines 403-408 [ggpt] (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:
  'ggplot2', 'rms', 'rsample', 'mice', 'mitml', 'dplyr', 'purrr',
  'tidyr', 'tibble', 'stringr', 'lme4', 'car'

Packages suggested but not available for checking: 'testthat', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘forecast’
Error(s) in re-building vignettes:
  ...
--- re-building ‘PSF_vignette.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PSF.Rcheck/vign_test/PSF/vignettes/PSF_vignette_files/figure-html/unnamed-chunk-6-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31420 bytes
Input file size = 31534 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 28614
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 28614

Output IDAT size = 28614 bytes (2806 bytes decrease)
Output file size = 28692 bytes (2842 bytes = 9.01% decrease)

** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PSF.Rcheck/vign_test/PSF/vignettes/PSF_vignette_files/figure-html/unnamed-chunk-7-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38585 bytes
Input file size = 38711 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 34198
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 34198

Output IDAT size = 34198 bytes (4387 bytes decrease)
Output file size = 34276 bytes (4435 bytes = 11.46% decrease)


Quitting from lines 100-150 [unnamed-chunk-8] (PSF_vignette.Rmd)
Error: processing vignette 'PSF_vignette.Rmd' failed with diagnostics:
there is no package called 'forecast'
--- failed re-building ‘PSF_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘PSF_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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) data1.Rd:14: Lost braces
    14 | The data set from {AbouRizk, S.M., Halpin, D.W., Wilson, J. R. (1994). \emph{Fitting beta distributions based on sample data.} Journal of Construction Engineering and Management 120(2), 288–305.}
       |                   ^
checkRd: (-1) data2.Rd:14: Lost braces; missing escapes or markup?
    14 | The data set presents the height of 99 five-year-old British boys in cm downloaded from {http://www.mas.ncl.ac.uk/njnsm/medfac/docs/intro.pdf.}
       |                                                                                         ^
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: 'intamap', 'automap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'asciiSetupReader', 'dplyr', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'DiagrammeR'

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’
checkRd: (-1) table1.Rd:14: Lost braces
    14 | The first data set from {Sulewski, P. (2017) \emph{A new test for independence in 2x2 contingency tables,} Acta Universitatis Lodziensis. Folia Oeconomica, 4(330), 55–75}
       |                         ^
checkRd: (-1) table3.Rd:14: Lost braces
    14 | The third data set from {Sulewski, P. (2021). \emph{Logarithmic Minimum Test for Independence in Three Way Con-tingency Table of Small Sizes.} Journal of Statistical Computation and Simulation 91(13), 2780-2799}
       |                         ^
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'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'admiral', 'dplyr', 'flexsurv', 'ggplot2', 'purrr', 'stringr',
  'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggsci', 'HMDHFDplus', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'dplyr', 'forcats', 'ggplot2', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AmesHousing', 'dplyr', 'ggplot2', '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 suggested but not available for checking: ‘testthat’
checkRd: (-1) pspGlobal.Rd:65-67: Lost braces
    65 |     \code{population}{The number of parameter sets in each ordinal region,
       |                      ^
checkRd: (-1) pspGlobal.Rd:68: Lost braces
    68 |     \code{iterations}{The number of global iterations. It has to be an integer. If emph{population} is not set or the regions have population less then the upper bound on their size, the function will stop after the set number of \emph{iterations}.}
       |                      ^
checkRd: (-1) pspGlobal.Rd:68: Lost braces
    68 |     \code{iterations}{The number of global iterations. It has to be an integer. If emph{population} is not set or the regions have population less then the upper bound on their size, the function will stop after the set number of \emph{iterations}.}
       |                                                                                        ^
checkRd: (-1) pspGlobal.Rd:69-71: Lost braces
    69 |     \code{lower, upper}{Vectors specifiying the lower and upper boundaries of
       |                        ^
checkRd: (-1) pspGlobal.Rd:72-74: Lost braces
    72 |     \code{init}{A marix of parameters to use as the first jumping distribution. 
       |                ^
checkRd: (-1) pspGlobal.Rd:75-76: Lost braces
    75 |     \code{radius}{The radius of the hypershere with n-dimensions to sample from.
       |                  ^
checkRd: (-1) pspGlobal.Rd:77-79: Lost braces
    77 |     \code{parameter_names}{A character vector that includes the names of each parameter.
       |                           ^
checkRd: (-1) pspGlobal.Rd:80-83: Lost braces
    80 |     \code{dimensionality}{A single integer that specifies the number of
       |                          ^
checkRd: (-1) pspGlobal.Rd:84-85: Lost braces
    84 |     \code{responses}{It is an integer that specifies the number of continuous
       |                     ^
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: ‘testthat’

Packages suggested but not available for checking: 'bench', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pillar', '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', 'EnvStats', 'epiR', 'ggplot2', 'longpower', 'plotly'

Packages suggested but not available for checking: 'MESS', 'WebPower'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘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
Package required but not available: ‘chngpt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GSVA', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'rstan', 'lme4', 'dplyr', 'purrr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'ggplot2'

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: 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'roxygen2', 'misty', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'progress', 'dplyr', 'tibble', 'tidyr', 'purrr'

Packages suggested but not available for checking: 'bib2df', 'testthat'

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.
Package suggested but not available for checking: ‘effects’
Packages required but not available:
  'qgraph', 'dplyr', 'optimx', 'VCA', 'IsingSampler', 'tidyr'

Packages suggested but not available for checking:
  'semPlot', 'graphicalVAR', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', '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: ‘likert’
Package suggested but not available for checking: ‘lme4’
Packages required but not available: 'broom', 'dplyr', 'ez'

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:
  > # PsychroLib (version 2.5.0) (https://github.com/psychrometrics/psychrolib).
  > # Copyright (c) 2018-2020 The PsychroLib Contributors. Licensed under the MIT License.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'bruceR', 'dplyr', 'stringr', 'purrr', 'vroom', 'ggplot2', 'ggrepel',
  'qgraph', 'text'

Packages suggested but not available for checking: 'wordsalad', 'sweater'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lme4', 'lmerTest', 'patchwork', 'stringr',
  'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'cowplot', 'ggrepel', 'interactions', 'qqplotr', 'roxygen2', 'see',
  'semPlot', 'testthat', 'lavaSearch2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'GGally', 'purrr', 'ggthemes',
  'fastDummies', 'ez', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DiagrammeR', 'haven', 'googlesheets4', 'readxl', 'testthat'
Running examples in ‘psyverse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_graph_theme
> ### Title: Apply multiple DiagrammeR global graph attributes
> ### Aliases: apply_graph_theme
> 
> ### ** Examples
> 
> exampleSpec <-
+   system.file("inst",
+               "extdata",
+               "example_dct_spec_1.dct",
+               package="psyverse");
> parsedSpecs <- load_dct_specs(exampleSpec);
> dctGraph <- parsedSpecs$output$basic_graph;
> dctGraph <- apply_graph_theme(dctGraph,
+                               c("color", "#0000AA", "node"),
+                               c("fillcolor", "#00FFFF", "node"));
Error: This function applies graph themes to a `DiagrammeR` object. Therefore, obviously, that object must first exist, and you need the `DiagrammeR` package to create it and work with it. Please install it using:

  install.packages('DiagrammeR');
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > require(testthat);
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > testthat::test_check("psyverse");
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'ggplot2', 'nloptr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) PTE_bootstrap_inference.Rd:39-42: Lost braces
    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
checkRd: (-1) PTE_bootstrap_inference.Rd:43-47: Lost braces
    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
checkRd: (-1) PTE_bootstrap_inference.Rd:48-52: Lost braces
    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
checkRd: (-1) PTE_bootstrap_inference.Rd:66-68: Lost braces
    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
checkRd: (-1) PTE_bootstrap_inference.Rd:74-77: Lost braces
    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
Packages suggested but not available for checking:
  'DiagrammeR', 'dplyr', 'readr', 'TITAN2', '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 ‘pTITAN2.Rmd’ using rmarkdown

Quitting from lines 331-336 [unnamed-chunk-3] (pTITAN2.Rmd)
Error: processing vignette 'pTITAN2.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘pTITAN2.Rmd’

SUMMARY: processing the following file failed:
  ‘pTITAN2.Rmd’

Error: Vignette re-building failed.
Execution halted
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:
  > 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.
Packages required but not available:
  'beepr', 'this.path', 'pryr', 'stringr'

Packages suggested but not available for checking:
  'ProjectTemplate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘BayesianTools’
Packages required but not available: 'purrr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ptw-package.Rd:20-28: Lost braces
    20 | @Article{Bloemberg2010,
       |         ^
checkRd: (-1) ptw-package.Rd:30-38: Lost braces
    30 | Article{Wehrens2015,
       |        ^
Packages required but not available:
  'ggplot2', 'ggdendro', 'htmlTable', 'R6P', 'reshape2', 'rmzqc',
  'UpSetR'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'stringr', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggformula', 'gtsummary', 'huxtable', 'car', 'dplyr', 'Epi', 'epiR',
  'ggplot2', 'moonBook', 'sjmisc', 'tibble', 'tidyselect'

Packages suggested but not available for checking:
  'broom', 'ggfortify', 'ggsci', 'Hmisc', 'jtools', 'latex2exp',
  'lme4', 'rms', 'rstatix', 'see', 'sjPlot', 'tidyverse'

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: 'purrr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'broom', 'DiagrammeR', 'dplyr', 'forcats', 'ggplot2', 'ggthemes',
  'gt', 'haven', 'infer', 'janitor', 'kableExtra', 'pkgdown', 'purrr',
  'roxygen2', 'rUM', 'stringr', 'tibble', 'tidyr', 'tidyverse',
  'testthat', 'vcdExtra'
Running ‘testthat.R’ [0s/1s]
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 ‘final.Rmd’ using rmarkdown

Quitting from lines 30-40 [tidyverse] (final.Rmd)
Error: processing vignette 'final.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘final.Rmd’

--- re-building ‘harmonization.Rmd’ using rmarkdown

Quitting from lines 306-326 [unnamed-chunk-1] (harmonization.Rmd)
Error: processing vignette 'harmonization.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘harmonization.Rmd’

SUMMARY: processing the following files failed:
  ‘final.Rmd’ ‘harmonization.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'purrr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'kableExtra', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'rvest', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'loo'

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:
  'riskRegression', 'testthat', 'rms'
Running examples in ‘Publish-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: splinePlot.lrm
> ### Title: Plot predictions of logistic regression
> ### Aliases: splinePlot.lrm
> 
> ### ** Examples
> 
> data(Diabetes)
> Diabetes$hypertension=  1*(Diabetes$bp.1s>140)
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bibliometrix’
'LazyData' is specified without a 'data' directory
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.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'dplyr', '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: 'ClusterR', 'igraph'

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:
  'batchtools', 'huge', 'network', 'testthat'
Running examples in ‘pulsar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findConfFile
> ### Title: find config file
> ### Aliases: findConfFile
> 
> ### ** Examples
> 
> ## Default config file provided by pulsar runs code in interactive mode
> ## This is for testing purposes and executes serially.
> findConfFile()
Error in loadNamespace(x) : there is no package called ‘batchtools’
Calls: findConfFile ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(testthat))
  Error in library(testthat) : there is no package called 'testthat'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
Packages required but not available:
  'dplyr', 'fda', 'fda.usc', 'ggplot2', 'monoClust', 'purrr', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'lubridate', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'lme4', 'purrr', 'readr', 'stringr',
  'tibble', 'tidyr', 'tidyselect'

Packages suggested but not available for checking:
  'furrr', 'kableExtra', '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:
  'dplyr', 'ggplot2', 'fda', 'stringr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'VWPre', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'colordistance', '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:
  'devtools', 'dplyr', 'ggplot2', 'readr', 'stringr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'profvis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'lme4'
'LazyData' is specified without a 'data' directory
Running ‘purged.filesizes.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: ‘progress’

Packages suggested but not available for checking:
  'caret', 'dplyr', 'ggplot2', 'ggraph', 'igraph', 'purrr', 'stringr',
  'testthat', 'tibble', 'tidyr', 'tidyselect'

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'

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:
  'dplyr', 'lubridate', 'testthat', 'tibble', 'tidyselect'

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 required but not available:
  'lubridate', 'readxl', 'reshape2', 'sqldf', 'kableExtra', 'dplyr',
  'tidyverse', 'readr'

Packages suggested but not available for checking: 'devtools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dcmle', 'dclone'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

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’
checkRd: (-1) DataSets.Rd:10: Lost braces; missing escapes or markup?
    10 | \format{the \code{PvarQuantileDF} is a \code{data.frame} with fields \code{prob} an {Qaunt}. 
       |                                                                                     ^
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: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'dtplyr', 'purrr', 'stringr', '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: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'progress', 'ggplot2', 'ggfittext'

Packages suggested but not available for checking:
  'furrr', 'plotly', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'broom', 'ggplot2', 'purrr', 'tidyr', '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: 'rumidas', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bibliometrix', 'igraph'

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', 'dplyr', 'tidyr', 'ez', 'phia', 'afex', 'MBESS', 'broom'

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
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch09-CDF-Pval.Rd:72: Lost braces; missing escapes or markup?
    72 |   G(u) = (1-r) u  + r Fc_A(Fc_0^{-1}(u))
       |                                 ^
checkRd: (-1) Ch10-CDF-Pval-HA.Rd:62: Lost braces; missing escapes or markup?
    62 |   G_A(u) = Fc_A(Fc_0^{-1}(u))
       |                      ^
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) Ch17-CRRtoRR.Rd:15: Lost braces; missing escapes or markup?
    15 |     \ldots, [t_m, t_{m+1})$ then \code{DT} will be c($t_2-t_1,t_3 -t_2,
       |                     ^
checkRd: (-1) Ch17-CRRtoRR.Rd:16: Lost braces; missing escapes or markup?
    16 |     \ldots, t_{m+1} - t_m )$
       |               ^
Packages suggested but not available for checking: 'roxygen2', 'testthat'
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available: 'stringr', '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: 'httptest', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > print(Sys.getenv("NOT_CRAN"))
  [1] ""
  > testthat::test_check("pxweb")
  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’
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', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'dbplyr', 'purrr', 'sparklyr', 'tidyselect', 'tidyr',
  'vctrs', 'httr2'

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’
'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
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', 'dplyr', 'tidyr', 'ggcorrplot', 'purrr', 'haven',
  'ggExtra', 'patchwork'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'viridis', 'ggExtra', 'dplyr', 'cowplot'

Packages suggested but not available for checking: 'reshape2', '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: 'lme4', 'dplyr', '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: 'mcmcse', 'stableGR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSQLite’

Package suggested but not available for checking: ‘async’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'purrr', 'stringr', 'tibble', 'httr2'

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', 'UpSetR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggforce', '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: 'stringr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘stringr’
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.
Packages required but not available: 'dplyr', 'purrr', 'qvalue', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cSEM', 'broom'

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.usc’

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', 'gender', 'ggplot2', 'igraph', 'reshape2', '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 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: 'regtools', 'toweranNA', 'partools'

Packages suggested but not available for checking:
  'keras', 'autoimage', 'cdparcoord'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Compositional', '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’
'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
'LazyData' is specified without a 'data' directory
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: 'qgcomp', 'arm', 'ggplot2'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'broom', 'devtools', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) QGlink.funcs.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGlink.funcs.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGlink.funcs.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:195: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:196: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:197: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:198: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:199: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:200: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:201: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:202: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:203: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:206: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'stringr', 'tibble', 'vctrs'

Packages suggested but not available for checking:
  'dplyr', 'spDataLarge', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Hmisc', 'igraph', 'reshape2', 'ggplot2'

Packages suggested but not available for checking: 'BDgraph', 'huge'

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: 'rms', '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: ‘ggplot2’

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: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) qif.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
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: ‘ggplot2’

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: ‘phytools’

Package suggested but not available for checking: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'alphahull', 'concaveman'

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: ‘ggplot2’
Running examples in ‘qlifetable-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.qlifetable
> ### Title: Graphical representation in a 4x4 raster of a qlifetable data
> ###   frame.
> ### Aliases: plot.qlifetable
> 
> ### ** Examples
> 
> dates.b <- c("1920-05-13", "1999-04-12", "2019-01-01")
> dates.e <- c("2002-03-23", "2009-04-12", "2019-01-01")
> x <- quarterly_variables(dates.b, dates.e)
> out <- time_exposed_outs(x)
> p <- plot(out, show.plot = FALSE)
Error in loadNamespace(x) : there is no package called ‘ggplot2’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'qad', 'ggplot2', 'cowplot', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) qmethod-package.Rd:109: Lost braces
   109 |   \item Van Exel, J., and G. de Graaf, 2005. \emph{Q Methodology: A Sneak Preview}\cr \url{https://qmethodblog.files.wordpress.com/2016/01/qmethodologyasneakpreviewreferenceupdate.pdf}{Available at this link}.
       |                                                                                                                                                                                         ^
checkRd: (-1) qmethod-package.Rd:110: Lost braces
   110 |   \item Brown, S. R., 1980. \emph{Political subjectivity: Applications of Q methodology in political science}, New Haven, CT: Yale University Press.\cr \url{https://qmethodblog.files.wordpress.com/2016/01/brown-1980-politicalsubjectivity.pdf}{Available at this link}.
       |                                                                                                                                                                                                                                                   ^
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:
  > # 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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'rstatix', 'ggpubr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'ggpmisc', 'ggthemes', 'kableExtra',
  'rstatix', '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
Specified C++11: please drop specification unless essential
Packages required but not available: 'dplyr', 'tidyr', '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:
  'dplyr', 'testthat', 'vdiffr'

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: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) hideLocation.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{trueLoc}{A vector of one or more numbers in the set {1, 2, ..., nSubjects} whose locations are to be hidden.}
       |                                                           ^
checkRd: (-1) hideLocation.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{nSubjects}{An integer larger than 1 used to define the set {1, 2, ..., nSubjects}.}
       |                                                                  ^
Packages required but not available: 'lme4', 'ggplot2'

Packages suggested but not available for checking:
  'glmmTMB', 'DHARMa', 'kableExtra', 'optimx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qrcm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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/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: 'Hmisc', 'ggplot2', 'rms', 'viridis'

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', '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:
  'desplot', 'dplyr', 'ggplot2', 'purrr', 'QBMS', 'readxl'

Packages suggested but not available for checking:
  'shinytest2', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qrmtools’
Package required but not available: ‘rugarch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘progress’

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: 'cowplot', 'ggplot2', 'purrr'

Packages suggested but not available for checking: 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DescTools', 'purrr'

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'
File ‘qs/libs/qs.so’:
  Found non-API calls to R: ‘SETLEVELS’, ‘SET_ENCLOS’, ‘SET_FRAME’,
    ‘SET_HASHTAB’, ‘SET_PRENV’, ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘correctness_testing.R’ [0s/1s]
  Running ‘qattributes_testing.R’ [0s/1s]
  Running ‘qsavemload_testing.R’ [0s/1s]
Running the tests in ‘tests/correctness_testing.R’ failed.
Complete output:
  > total_time <- Sys.time()
  > 
  > suppressMessages(library(Rcpp))
  > suppressMessages(library(dplyr))
  Error in library(dplyr) : there is no package called 'dplyr'
  Calls: suppressMessages -> withCallingHandlers -> library
  Execution halted
Running the tests in ‘tests/qattributes_testing.R’ failed.
Complete output:
  > total_time <- Sys.time()
  > 
  > suppressMessages(library(Rcpp))
  > suppressMessages(library(dplyr))
  Error in library(dplyr) : there is no package called 'dplyr'
  Calls: suppressMessages -> withCallingHandlers -> library
  Execution halted
Running the tests in ‘tests/qsavemload_testing.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'RSQLite', 'dplyr', 'dbplyr', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'readr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'BMisc', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qtl2’

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qtl2’

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', 'stringr', 'tidyr', 'qtl2', 'ggrepel'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'stringr', 'ggplot2', 'qtl2', 'qtl2fst'

Package suggested but not available for checking: ‘qtl2ggplot’

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:
  'testthat', 'broman', 'devtools', 'qtl2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSQLite’

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'
Running ‘Rmdtest.R’ [0s/0s]
  Running ‘htmltest.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: 'stringr', 'QTL.gCIMapping'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readxl', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'sem', 'pcalg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'RLRsim', 'mappoly'

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 ‘test_io.R’ [1s/1s]
  Comparing ‘test_io.Rout’ to ‘test_io.Rout.save’ ... OK
  Running ‘test_mapqtl_io.R’ [3s/4s]
  Comparing ‘test_mapqtl_io.Rout’ to ‘test_mapqtl_io.Rout.save’ ... OK
  Running ‘test_qtl.R’ [4s/6s]
  Running ‘test_scanonevar.R’ [8s/9s]
  Comparing ‘test_scanonevar.Rout’ to ‘test_scanonevar.Rout.save’ ... OK
  Running ‘test_tidyIO.R’ [0s/1s]
  Comparing ‘test_tidyIO.Rout’ to ‘test_tidyIO.Rout.save’ ... OK
  Running ‘testaugmentation.R’ [2s/3s]
  Running ‘testthat.R’ [0s/1s]
Running 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', 'faraway', 'quantoptr', 'survminer'
checkRd: (-1) IPWE_mean_IndCen.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
checkRd: (-1) simJLSDdata.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mice’
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'kableExtra', 'testthat', 'tidyr', 'viridis'
Running ‘testthat.R’ [0s/1s]
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 ‘cleaning_coral.Rmd’ using rmarkdown

Quitting from lines 27-37 [load package] (cleaning_coral.Rmd)
Error: processing vignette 'cleaning_coral.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘cleaning_coral.Rmd’

--- re-building ‘cleaning_cropping_coral.Rmd’ using rmarkdown

Quitting from lines 35-46 [load package] (cleaning_cropping_coral.Rmd)
Error: processing vignette 'cleaning_cropping_coral.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘cleaning_cropping_coral.Rmd’

--- re-building ‘cropping.Rmd’ using rmarkdown

Quitting from lines 34-38 [load package] (cropping.Rmd)
Error: processing vignette 'cropping.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘cropping.Rmd’

--- re-building ‘function_examples.Rmd’ using rmarkdown
--- finished re-building ‘function_examples.Rmd’

SUMMARY: processing the following files failed:
  ‘cleaning_coral.Rmd’ ‘cleaning_cropping_coral.Rmd’ ‘cropping.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
'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: 'ggpp', 'ggplot2', 'ggpubr'

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:
  > # 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', '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’
checkRd: (-1) find_lcp.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:18-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'janitor', 'readxl'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tigris', 'tidycensus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) qualpal.Rd:22-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qualpal.Rd:30-50: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'purrr', 'readr', 'stringr', '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:
  'dplyr', 'tidyr', 'ggplot2', 'GGally'
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown

Quitting from lines 111-120 [correlation] (wilcox1973.Rmd)
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
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: 'lubridate', 'quantdates'

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: ‘lubridate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
checkRd: (-1) cqs.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:37-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:38-41: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/1s]
Running 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:
  'dplyr', 'purrr', 'stm', 'tibble', 'tidytext'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'quanteda.textplots', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...5c5
< 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:
  'ggplot2', 'ggrepel', 'sna', 'igraph', 'network'

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:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > 
  > 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: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'kableExtra', '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 ‘QuantileNPCI.Rmd’ using rmarkdown

Quitting from lines 35-38 [setup] (QuantileNPCI.Rmd)
Error: processing vignette 'QuantileNPCI.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘QuantileNPCI.Rmd’

SUMMARY: processing the following file failed:
  ‘QuantileNPCI.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'vctrs', 'tidyr', '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
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: ‘RSQLite’
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Packages suggested but not available for checking:
  'GGally', 'ggplot2', 'network', 'sna'
Running examples in ‘QuantNorm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: connection.matrix
> ### Title: Construct connection matrix for network analysis
> ### Aliases: connection.matrix
> 
> ### ** Examples
> 
> 
> library(network); library(ggplot2); library(sna); library(GGally) #drawing network graph
Error in library(network) : there is no package called ‘network’
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'

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: ‘fda’

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’
checkRd: (-1) MovingBlocks-class.Rd:11: Lost braces
    11 | bootstrap described in K{\"u}nsch (1989).
       |                         ^
checkRd: (-1) MovingBlocks-class.Rd:18: Lost braces
    18 | The Moving Blocks Bootstrap method of K{\"u}nsch (1989) resamples blocks
       |                                        ^
checkRd: (-1) MovingBlocks-class.Rd:25: Lost braces
    25 | K{\"u}nsch, H. R. (1989). The jackknife and the bootstrap for general stationary
       |  ^
checkRd: (-1) frequenciesValidator.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{steps}{a vector containing a subset of {1,2,3,4,5,6}, indicating
       |                                              ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'rugarch', 'smoots', 'yfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) quarries.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:26-28: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking:
  'phangorn', 'testthat', 'usethis', '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
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 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: 'styler', 'labelled'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'dplyr', 'ggplot2', 'tidyr', 'janitor',
  'forcats', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'MBESS', 'lme4'

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: 'tidyr', '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
Packages required but not available:
  'testthat', 'hedgehog', 'purrr', 'tibble', 'hms'

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:
  > # 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
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘testthat’
File ‘quickmatch/libs/quickmatch.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
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:
  'fastshp', 'ggplot2', 'testthat'
Running examples in ‘quickPlot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: whereInStack
> ### Title: Find the environment in the call stack that contains an object
> ###   by name
> ### Aliases: whereInStack
> 
> ### ** Examples
> 
> b <- 1
> inner <- function(y) {
+   objEnv <- whereInStack("b")
+   get("b", envir = objEnv)
+ }
> findB <- function(x) {
+   b <- 2
+   inner()
+ }
> findB() # Finds 2 because it is looking up the call stack, i.e., the user's perspective
[1] 2
> 
> # defined outside of findB2, so its enclosing environment is the same as findB2
> innerGet <- function(y) {
+    get("b")
+ }
> findB2 <- function(x) {
+   b <- 2
+   innerGet()
+ }
> findB2() # Finds 1 because b has a value of 1 in the enclosing environment of innerGet
[1] 1
> b <- 3
> findB2() # Finds 3 because b has a value of 3 in the enclosing environment of innerGet,
[1] 3
>          #  i.e., the environment in which innerGet was defined
> findB() # Still finds 2 because the call stack hasn't changed
[1] 2
> 
> # compare base::dynGet
> findB3 <- function(x) {
+   b <- 2
+   dynGet("b")
+ }
> findB3() # same as findB(), but marginally faster, because it omits the stripping on
[1] 2
>          #   sub elements that may be part of the name argument
> 
> 
> b <- list()
> findB3 <- function(x) {
+   b$a <- 2
+   dynGet("b$a")
+ }
> testthat::expect_error(findB3()) # fails because not an object name
Error in loadNamespace(x) : there is no package called ‘testthat’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
coordinates 5.945  0.091   7.524
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 ‘iii-plotting.Rmd’ due to unavailable dependencies:
  'ggplot2'
Packages required but not available: 'dplyr', '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: 'ggplot2', 'dplyr'

Packages suggested but not available for checking: 'ggthemes', '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 suggested but not available for checking: ‘adegenet’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'BayesFactor', 'janitor', 'purrr', 'stringr', 'dplyr', 'ggplot2',
  '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 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:
  'stringr', 'vroom', 'purrr', 'dplyr', 'tidyjson', 'tibble',
  'lubridate', 'tidyr', 'rvest', 'progress'

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:
  'dplyr', 'ggplot2', 'rsample', 'tibble', 'tidyselect'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

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
'LazyData' is specified without a 'data' directory
File ‘quotedargs/libs/quotedargs.so’:
  Found non-API calls to R: ‘SETLEVELS’, ‘SET_NAMED’, ‘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.
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', 'stringr', 'tidyr', 'drc', 'ggh4x', 'ggnewscale', 'ggplot2',
  'ggpubr', 'kableExtra', 'purrr', 'readxl'

Packages suggested but not available for checking:
  'shinyFiles', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GDINA', 'nloptr'

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/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: ‘ggplot2’

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: ‘fda’
Running examples in ‘QZ-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fda.geigen
> ### Title: Generalized Eigen Analysis as in fda Package
> ### Aliases: fda.geigen
> ### Keywords: programming
> 
> ### ** Examples
> 
> library(QZ, quiet = TRUE)
> 
> A <- matrix(as.double(1:6), 2)
> B <- matrix(as.double(c(2, 1, 1, 2)), 2)
> C <- diag(as.double(1:3))
> 
> ret.qz <- fda.geigen(A, B, C)
> 
> ### Verify
> library(fda, quiet = TRUE)
Error in library(fda, quiet = TRUE) : there is no package called ‘fda’
Execution halted
checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'lme4', 'ggplot2', 'testthat'
checkRd: (-1) do_admb.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_pars.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
Note: skipping ‘R2admb.Rnw’ due to unavailable dependencies: 'ggplot2'
Package suggested but not available for checking: ‘ReGenesees’
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) conf2d.Rd:64: Lost braces; missing escapes or markup?
    64 |   compute a smooth surface from \code{x} and {y}. If users already have
       |                                              ^
Packages suggested but not available for checking: 'shinytest', '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’

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:
  'r2dii.match', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'charlatan', 'readr', 'testthat'
Error in FUN(X[[i]], ...) : cannot return a promise (PROMSXP) object
Calls: <Anonymous> -> Filter -> unlist -> lapply -> FUN
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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', 'purrr', '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:
  'dplyr', 'ggplot2', 'ggrepel', 'stringr'

Packages suggested but not available for checking:
  'r2dii.analysis', 'r2dii.match', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devFunc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lmerTest', 'pbkrtest', 'ggplot2', 'afex', 'dplyr'

Packages suggested but not available for checking: 'lme4', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) HTML.data.frame.Rd:54: Lost braces; missing escapes or markup?
    54 |         \code{getOption("R2HTML.format.decimal.mark")} and {options("R2HTML.format.decimal.mark"=",")}
       |                                                            ^
Rd file 'HTMLInsertGraph.Rd':
  \examples lines wider than 100 characters:
             ## Not run: plot(table(rpois(100,5)), type = "h", col = "red", lwd=10,main="rpois(100,lambda=5)")

These lines will be truncated in the PDF 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:
  'lme4', 'dplyr', 'rockchalk', 'stringr', 'tidyselect'

Packages suggested but not available for checking: 'bootmlm', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom', 'tibble'

Packages suggested but not available for checking: 'doBy', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
checkRd: (-1) bugs.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:166: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'caret', 'mlr'
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 ‘basic_usage.Rmd’ using rmarkdown

Quitting from lines 18-20 [setup] (basic_usage.Rmd)
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘basic_usage.Rmd’

--- re-building ‘templates.Rmd’ using rmarkdown
--- finished re-building ‘templates.Rmd’

SUMMARY: processing the following file failed:
  ‘basic_usage.Rmd’

Error: Vignette re-building failed.
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 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', 'testthat', 'tidyr'
Running examples in ‘r2rtf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rtf_body
> ### Title: Add Table Body Attributes to the Table
> ### Aliases: rtf_body
> 
> ### ** Examples
> 
> library(dplyr) # required to run examples
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running 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: ‘stringr’

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: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Packages suggested but not available for checking:
  'colourpicker', '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: ‘vctrs’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'BayesianTools', 'sensitivity', '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 required but not available: ‘reshape2’

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'roxygen2', 'testthat'
Package required but not available: ‘tutorial.helpers’

Packages suggested but not available for checking:
  'arrow', 'babynames', 'dbplyr', 'dplyr', 'gghighlight', 'ggrepel',
  'ggridges', 'ggthemes', 'janitor', 'nycflights13', 'patchwork',
  'readxl', 'repurrrsive', 'rvest', 'socviz', 'testthat', 'tidymodels',
  'tidyverse', 'usethis', 'Lahman', 'RPostgres', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'magick', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'stringr', 'kableExtra'

Packages suggested but not available for checking:
  'testthat', 'reshape2', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘concaveman’

Packages suggested but not available for checking:
  'accessibility', 'dplyr', 'ggplot2', 'h3jsr', 'patchwork', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pkgdown', '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: 'causaleffect', 'igraph'

Packages suggested but not available for checking: 'qgraph', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘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', 'stringr', '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'

Packages suggested but not available for checking:
  'ggplot2', 'RSQLite', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'pryr'
Running ‘testthat.R’ [0s/1s]
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) post_RA_fits.Rd:61: Lost braces; missing escapes or markup?
    61 |     \item{\code{H(po_{bm_{n.bm}}, po_act)}:}{ last benchmark prior bm_{n.bm} inducing the fit \code{fits.bm[[n.bm]]} and actual prior}
       |                                                                       ^
'LazyData' is specified without a 'data' directory
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', 'httr2', 'purrr', 'stringr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'harmony', 'igraph', 'leiden'

Packages suggested but not available for checking:
  'batchelor', 'DESeq2', 'slingshot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dplyr', 'testthat'
Running examples in ‘raceland-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_metrics
> ### Title: Calculate Metrics
> ### Aliases: calculate_metrics
> 
> ### ** Examples
> 
> library(terra)
terra 1.7.78
> race_raster = rast(system.file("extdata/race_raster.tif", package = "raceland"))
> x = create_realizations(race_raster, n = 5)
> w = create_densities(x, race_raster, window_size = 10)
> 
> #1
> df = calculate_metrics(x, w, neighbourhood = 4, fun = "mean")
> 
> #2
> df2 = calculate_metrics(x, w, neighbourhood = 4, fun = "mean", size = 10, threshold = 0.5)
> my_grid = create_grid(x, size = 10)
> 
> df3 = dplyr::filter(df2, realization == 2)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
calculate_densities 7.158  0.092   9.789
Running ‘testthat.R’ [0s/1s]
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 ‘raceland-intro1.Rmd’ using rmarkdown

Quitting from lines 76-81 [unnamed-chunk-4] (raceland-intro1.Rmd)
Error: processing vignette 'raceland-intro1.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘raceland-intro1.Rmd’

--- re-building ‘raceland-intro2.Rmd’ using rmarkdown

Quitting from lines 49-53 [unnamed-chunk-3] (raceland-intro2.Rmd)
Error: processing vignette 'raceland-intro2.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘raceland-intro2.Rmd’

--- re-building ‘raceland-intro3.Rmd’ using rmarkdown
--- finished re-building ‘raceland-intro3.Rmd’

SUMMARY: processing the following files failed:
  ‘raceland-intro1.Rmd’ ‘raceland-intro2.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:
  'shinyFiles', 'ggplot2', 'igraph', 'dplyr', 'vctrs'

Packages suggested but not available for checking:
  'testthat', 'r3js', 'plotly', 'readxl', 'stringr', 'tibble', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'tidyr'

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', '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 ‘preparingData.Rmd’ using rmarkdown

Quitting from lines 28-32 [tidyR] (preparingData.Rmd)
Error: processing vignette 'preparingData.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building ‘preparingData.Rmd’

SUMMARY: processing the following file failed:
  ‘preparingData.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'lme4', 'ggplot2', 'reshape2', 'lmerTest', 'tidyr', 'stringr',
  'dplyr', 'Hmisc', 'car'

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: ‘radsafer’
Packages required but not available: 'ggplot2', 'tidyr', 'dplyr', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'radiant.data', 'ggplot2', 'dplyr', 'tidyr', 'lubridate', 'patchwork'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'tidyr', 'dplyr', 'tibble', 'arrow', 'broom',
  'car', 'readr', 'readxl', 'plotly', 'shinyFiles', 'patchwork'

Packages suggested but not available for checking:
  'dbplyr', 'RSQLite', 'RPostgres', 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'radiant.data', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'radiant.data', 'radiant.basics', 'NeuralNetTools', 'car', 'ggplot2',
  'stringr', 'lubridate', 'tidyr', 'dplyr', 'tidyselect', 'DiagrammeR',
  'ggrepel', 'broom', 'patchwork', 'pdp', 'vip'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'radiant.data', 'radiant.model', 'dplyr', 'ggplot2', 'car',
  'ggrepel', 'lubridate', 'clustMixType', 'patchwork'

Packages suggested but not available for checking: 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'radiant.data', 'radiant.design', 'radiant.basics', 'radiant.model',
  'radiant.multivariate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lexicon', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot-methods.Rd:98: Lost braces
    98 |                         The line width, a emph{positive} number, defaulting to \code{1}. The interpretation is device-specific, and some devices do not implement line widths less than one (see the help on the device for details of the interpretation). Note that this paramater can also represent a list of different line widths, with length of the list corresponding to the number of \code{DVH} or \code{DVH.list} objects (if \code{plot.type="individual"}, number of line widths should correspond to number of individual \code{DVH} objects).
       |                                               ^
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:
  'ggplot2', 'readr', 'stringr', 'dplyr', 'ggthemes'

Packages suggested but not available for checking: 'testthat', 'beepr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vcfR', 'ggplot2', 'ggridges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'igraph'

Packages suggested but not available for checking: 'tidyr', 'cytofan'

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 required but not available: ‘DiagrammeR’

Packages suggested but not available for checking:
  'ggplot2', 'Rcompadre', '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: 'igraph', 'ggplot2', 'Hmisc', 'gRbase'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'reshape2', 'stringr', '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 ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown

Quitting from lines 20-33 [global_options] (ragtop_convertibles_in_r.Rmd)
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

SUMMARY: processing the following file failed:
  ‘ragtop_convertibles_in_r.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘hdrcde’

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'stringr', 'MM4LMM'

Packages suggested but not available for checking:
  'plotly', 'haplotypes', 'adegenet', 'ggplot2', 'ggtree',
  'scatterpie', 'phylobase', 'furrr'

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:
  'dplyr', 'tidyr', 'purrr', 'ggplot2', 'stringr', 'dendextend',
  'ggwordcloud'

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
Packages required but not available: 'dplyr', 'ggplot2', '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: 'tibble', 'dplyr', 'progress'

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', 'cowplot', 'reshape2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'readr'
'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', 'tidyr', 'dplyr', 'stringr', 'robotstxt'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'haven', 'Hmisc', 'ggplot2', 'readr', 'shinyFiles', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'ggrepel', 'imputeTS'

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: 'lubridate', 'stringr'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'lubridate'
checkRd: (-1) DataSet-class.Rd:25: Lost braces; missing escapes or markup?
    25 | Example: {fromField:"val1", toField:"value"}.}
       |          ^
checkRd: (-1) amTimeSeries.Rd:119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getCurrentStockData.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getCurrentStockData.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTransformTS.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTransformTS.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:156: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:38: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'webchem', 'ggplot2'

Packages suggested but not available for checking:
  'xcms', 'testthat', 'patrick', 'MSnbase', 'readxl'

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: 'lubridate', '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
Package required but not available: ‘readxl’

Packages suggested but not available for checking: 'testthat', 'httptest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'tidyverse', 'ggplot2', 'dplyr', 'plotly', 'RSQLite',
  'arrow', 'rvest'
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 ‘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
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sparseFLMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'stringr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'diffdf', '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', 'GGally', 'ggplot2', 'ggrepel', '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', '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 ‘RandomForestsGLS_user_guide.Rmd’ using rmarkdown

Quitting from lines 153-170 [plot_comparison] (RandomForestsGLS_user_guide.Rmd)
Error: processing vignette 'RandomForestsGLS_user_guide.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘RandomForestsGLS_user_guide.Rmd’

SUMMARY: processing the following file failed:
  ‘RandomForestsGLS_user_guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘DiagrammeR’

Packages suggested but not available for checking:
  'pec', 'caret', 'imbalance'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking: 'EZtune', '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:
  'ggplot2', 'purrr', 'dplyr', 'gsDesign', '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: 'dplyr', 'testthat'
File ‘randomizr/libs/randomizr.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 ‘randomizr_vignette.Rmd’ using rmarkdown

Quitting from lines 444-461 [unnamed-chunk-56] (randomizr_vignette.Rmd)
Error: processing vignette 'randomizr_vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘randomizr_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘randomizr_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) outcomeProbs.Rd:18: Lost braces
    18 |   \item{scale}{either "prob" where probabilities are returned, the default, or "raw" where the probabilities are returned on the logit or probit scale, depending on which scale was selected in the texttt{randomLCA} function}
       |                                                                                                                                                                                                            ^
Package required but not available: ‘toOrdinal’

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: ‘dplyr’
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: ‘caret’

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 ‘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) auxfun.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:38-44: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘alphahull’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSQLite’

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'viridis', 'pkgdown', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spocc’

Packages suggested but not available for checking:
  'googlesheets4', 'rgbif', '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
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vctrs’

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: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 suggested but not available for checking: ‘rms’
Running examples in ‘rankhazard-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankhazard-package
> ### Title: Rank-hazard plots
> ### Aliases: rankhazard-package rankhazard
> ### Keywords: package hplot survival
> 
> ### ** Examples
> 
> library(survival)
> model <- coxph(Surv(time,status) ~ age + sex + ph.karno, data = cancer, x=TRUE)
> rankhazardplot(model, data=cancer)
Y-axis range:  0.608 1.49 
 
Relative hazards for each covarite: 
          Min. 1st Qu. Median 3rd Qu. Max.
age      0.743   0.917      1    1.08 1.27
sex      0.608   0.608      1    1.00 1.00
ph.karno 0.766   0.875      1    1.07 1.49
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Package required but not available: ‘netmeta’

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: ‘viridis’

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 suggested but not available for checking:
  'devtools', 'ggplot2', 'reshape2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown

Quitting from lines 34-35 [unnamed-chunk-3] (overview.Rmd)
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘overview.Rmd’

--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 22-26 [unnamed-chunk-2] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘overview.Rmd’ ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) rankL2R.Rd:18: Lost braces; missing escapes or markup?
    18 | where the vector dimension is 2^{response.number}.}
       |                                 ^
Package required but not available: ‘randomForestSRC’

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
'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: 'dplyr', 'bigsnpr', 'coloc'

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 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', 'httr2', 'lubridate', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking: 'devtools', '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: 'roxygen2', 'testthat'
checkRd: (-1) user_log_dir.Rd:48: Lost braces
    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
Running ‘testthat.R’ [0s/1s]
Running 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: 'stringr', 'rapportools'

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: 'stringr', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tibble', 'dplyr', 'RSQLite'

Packages suggested but not available for checking: 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'ggplot2', 'hypervolume'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'dplyr', 'gurobi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'stringr', 'tibble'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httr2’

Package suggested but not available for checking: ‘tibble’

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.
Packages required but not available:
  'dplyr', 'stringr', 'tidyr', 'reshape2', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dendextend’
Packages required but not available:
  'dplyr', 'ggplot2', 'latex2exp', 'patchwork', 'tidyr', '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
Packages required but not available:
  'dplyr', 'purrr', 'tibble', 'tidyr', 'tidyselect', 'vctrs',
  'testthat'

Packages suggested but not available for checking:
  'broom', 'forcats', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pins’

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: '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
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'GGally', '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: ‘bcmaps’
Packages required but not available:
  'ggforce', 'ggplot2', 'progress', 'viridis'

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', 'lubridate', 'ggplot2', 'knitcitations', 'lmomPi',
  'stringr'
checkRd: (-1) RasterList-Package.Rd:20: Lost braces
    20 | {\code{\link{rasterList}}}{: it is the constructor of a  \code{\link{RasterList-class}} object from a generic \code{object}, it also transforms a \code{\link{RasterList-class}} into another one throungh a function argument. }
       |                           ^
checkRd: (-1) RasterList-Package.Rd:22: Lost braces
    22 | {\code{\link{rasterListFun}}}{: it is a function that constructs  a  particular \code{\link{RasterList-class}} object in which the objects are \code{function}-type. }
       |                              ^
checkRd: (-1) RasterList-Package.Rd:24: Lost braces
    24 | {\code{\link{RasterListApply}}}{: it is a function that allows to operate among two or more \code{\link{RasterList-class}} objects defined in the same spatial extent through a generic function \code{fun(x,y,...)} where \code{x} and \code{y} are each cell/element of two \code{\link{RasterList-class}} objects given as arguments \code{x} and \code{y} of \code{\link{RasterListApply}}.}
       |                                ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘rasterList_vignette_004.Rmd’ using rmarkdown

Quitting from lines 295-307 [unnamed-chunk-24] (rasterList_vignette_004.Rmd)
Error: processing vignette 'rasterList_vignette_004.Rmd' failed with diagnostics:
there is no package called 'lubridate'
--- failed re-building ‘rasterList_vignette_004.Rmd’

SUMMARY: processing the following file failed:
  ‘rasterList_vignette_004.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'pkgdown', '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', 'tidyterra'
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 ‘rasterpic.Rmd’ using rmarkdown

Quitting from lines 29-47 [setup] (rasterpic.Rmd)
Error: processing vignette 'rasterpic.Rmd' failed with diagnostics:
there is no package called 'tidyterra'
--- failed re-building ‘rasterpic.Rmd’

SUMMARY: processing the following file failed:
  ‘rasterpic.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘igraph’
Running examples in ‘raster-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clump
> ### Title: Detect clumps
> ### Aliases: clump clump,RasterLayer-method
> ### Keywords: spatial
> 
> ### ** Examples
> 
> r <- raster(ncols=12, nrows=12)
> set.seed(0)
> values(r) <- round(runif(ncell(r))*0.7 )
> rc <- clump(r) 
Loading required namespace: igraph
Failed with error:  ‘there is no package called ‘igraph’’
Error in .local(x, ...) : 
  you need to install the igraph package to be able to use this function
Calls: clump -> clump -> .local
Execution halted
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available: 'ggplot2', 'Rirt', '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’
Running ‘testthat.R’ [0s/1s]
Running 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: 'geiger', 'readr', 'mvMORPH'

Package suggested but not available for checking: ‘phytools’

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 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 suggested but not available for checking:
  'arrow', 'dplyr', 'dbplyr', 'testthat', 'tibble', 'vroom'
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:109-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:115-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:121-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:125-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:128-138: Lost braces in \itemize; meant \describe ?
Running examples in ‘RAthena-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RAthena_options
> ### Title: A method to configure RAthena backend options.
> ### Aliases: RAthena_options
> 
> ### ** Examples
> 
> library(RAthena)
> 
> # change file parser from default data.table to vroom
> RAthena_options("vroom")
Error: Please install vroom package 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
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) S1.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{m_bar}{the sample vector of moments for a specified vector $(h_{a,r},y)$}
       |                                                                      ^
checkRd: (-1) S1.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{N_k}{index of the $ h_{a,r}$ function considered}
       |                             ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘qspray’

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: 'ggplot2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tibblify', '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:
  'tibble', 'ggplot2', 'stringr', 'tidyr', 'dplyr'

Packages suggested but not available for checking:
  'pmml', 'arulesViz', 'biclust', 'cairoDevice', 'doBy', 'ggdendro',
  'Hmisc', 'janitor', 'mice', 'RGtk2', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlogit', 'dfidx', 'bedr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tibble', 'purrr', '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
Packages required but not available:
  'cowplot', 'DiagrammeR', 'dplyr', 'ggplot2', 'igraph', 'lubridate',
  'purrr', 'stringr', 'tidyr'

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 ‘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', 'ggplot2', 'kableExtra', 'plotly', 'purrr'

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 suggested but not available for checking:
  'ChainLadder', 'dplyr', 'devtools', 'FinCal', 'forcats', 'ggplot2',
  'Lahman', 'lubridate', 'nycflights13', 'purrr', 'randomNames',
  'readr', 'readxl', 'stringr', 'tibble', 'tidyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘raw.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/raw.Rcheck/vign_test/raw/vignettes/raw_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3980 bytes
Input file size = 4838 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 3471
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 3447
  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 = 3447

Output IDAT size = 3447 bytes (533 bytes decrease)
Output file size = 3525 bytes (1313 bytes = 27.14% decrease)


Quitting from lines 150-153 [unnamed-chunk-10] (raw.Rmd)
Error: processing vignette 'raw.Rmd' failed with diagnostics:
there is no package called 'lubridate'
--- failed re-building ‘raw.Rmd’

SUMMARY: processing the following file failed:
  ‘raw.Rmd’

Error: Vignette re-building failed.
Execution halted
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: 'progress', 'rayvertex'

Packages suggested but not available for checking:
  'rayrender', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘progress’

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: 'rayrender', 'rayvertex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rayimage', 'progress', 'rayvertex', 'vctrs', 'pillar'

Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'progress', 'rayimage', 'rayvertex', 'rayrender'

Packages suggested but not available for checking:
  'reshape2', 'viridis', 'magick', 'ggplot2', 'car', 'elevatr',
  'testthat', 'osmdata', 'raybevel'

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: ‘rayimage’

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:
  'stringr', 'readr', 'dplyr', 'rvest', 'purrr', 'readxl', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 required but not available: 'purrr', 'tidyr', 'dplyr', 'ggplot2'

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', 'dplyr'

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.
checkRd: (-1) ecoperators-methods.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:54: Lost braces in \itemize; meant \describe ?
Found the following HTML validation problems:
getblock.html:58:1 (getblock.Rd:23): Warning: trimming empty <h3>
getrawtransaction.html:57:1 (getrawtransaction.Rd:22): Warning: trimming empty <h3>
Package suggested but not available for checking: ‘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:
  'tibble', 'stringr', 'dplyr', 'purrr', 'readr', 'vctrs', '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:
  'rstan', 'bayesplot', 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'purrr', 'rstanarm', 'broom', 'tidyr', 'brms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) rbeta.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rbeta.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rbeta.Rd:35-37: Lost braces in \itemize; meant \describe ?
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.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'ggpubr', '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: 'rbi', 'lubridate', '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', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'rstan', 'ggmcmc', 'GGally', 'loo', '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 suggested but not available for checking: '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
Package required but not available: ‘reshape2’

Packages suggested but not available for checking: 'testthat', 'ggplot2'

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: 'mmrm', 'rstan'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'testthat', 'tibble', 'lubridate', 'purrr',
  '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: 'lubridate', 'readxl', 'rvest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘imbalance’

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: ‘mlr’

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 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) ecoperators-methods.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:54: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
getblock.html:58:1 (getblock.Rd:23): Warning: trimming empty <h3>
getrawtransaction.html:57:1 (getrawtransaction.Rd:22): Warning: trimming empty <h3>
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package 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) R.cache-package.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) R.cache-package.Rd:31-34: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘testthat’

Packages suggested but not available for checking:
  'autothresholdr', 'imager'

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’
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.
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/1s]
Running 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:
  'optmatch', 'testthat', 'rrelaxiv'
Running ‘testthat.R’ [0s/1s]
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:
  'rstan', 'dplyr', 'tibble', 'tidybayes'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rrelaxiv', 'optmatch'
Running ‘testthat.R’ [0s/1s]
Running 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: ‘redcapAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
Package suggested but not available for checking: ‘devtools’
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 suggested but not available for checking: 'testthat', 'devtools'
'LazyData' is specified without a 'data' directory
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', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) nc_open_CGLS.Rd:29-32: Lost braces
    29 | if(resolution == "300m"){
       |                         ^
checkRd: (-1) nc_open_CGLS.Rd:33-36: Lost braces
    33 | if(resolution == "1km"){
       |                        ^
'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/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/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/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:
  'oceanmap', 'readr', 'lubridate', 'stringr', 'ggplot2', 'ggedit',
  'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'AER'
checkRd: (-1) Rchoice.Rd:159: Lost braces; missing escapes or markup?
   159 |  \code{ranp}. If the parameters are assumed to be normally distributed \eqn{\beta_i ~ N(\beta, \Sigma)}, then the random parameter are constructed as: \deqn{\beta_{ir}=\beta+L\omega_{ir}} where \eqn{LL'=\Sigma} and \eqn{\omega_{ir}} is the {r}-th draw from standard normal distribution for individual \eqn{i}. 
       |                                                                                                                                                                                                                                                 ^
Package required but not available: ‘hdrcde’

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 suggested but not available for checking: 'testthat', 'tibble'
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: 'Hmisc', 'purrr'

Packages suggested but not available for checking:
  'dplyr', 'stringr', 'testthat', 'tibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'dbplyr'

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', 'tibble', 'lubridate', 'tidyr', 'tidyselect'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'factoextra', 'FactoMineR', 'ggplot2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘outcmaesdisp.dat’
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
Packages required but not available: 'car', 'Hmisc', 'haven', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'biclust', 'iBBiG', 'superbiclust', 'BicARE', 's4vd', 'BiBitR',
  'Rcmdr', 'viridis'

Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcmdrMisc', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FrF2', 'DoE.wrapper', 'Rcmdr', 'RcmdrMisc'

Package suggested but not available for checking: ‘FrF2.catlg128’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ez', 'Rcmdr', 'RcmdrMisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'epiR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Packages suggested but not available for checking:
  'car', 'ggplot2', 'meta', 'netmeta', 'plotly', 'tableone', 'readxl',
  'lmerTest', 'swimplot', 'rstatix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcmdrMisc', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'HH', 'Rcmdr'

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'ggplot2', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixlm', 'phia', 'Rcmdr', 'car'

Packages suggested but not available for checking: 'lme4', 'pbkrtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcmdr', 'demography', 'forecast', 'ftsa', 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'Hmisc', 'lme4'

Package suggested but not available for checking: ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Packages suggested but not available for checking:
  'ROpenOffice', 'tm.plugin.factiva'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qicharts2', 'Rcmdr'

Package suggested but not available for checking: ‘car’

Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Package suggested but not available for checking: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcmdrMisc', 'car', 'effects', 'lme4'

Packages suggested but not available for checking: 'Hmisc', 'readxl', 'sem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) nonlinearAR1.sim.Rd:8: Lost braces; missing escapes or markup?
     8 | of the form z_n = g(z_{n-1}) + epsilon. A normal distribution is assumed for the innovations.
       |                       ^
Packages required but not available: 'qgraph', '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: ‘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: ‘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
Package required but not available: ‘tibble’

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'rcrossref', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'gh', 'stringr', 'usethis'

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: ‘conics’
Packages required but not available:
  'readr', 'dplyr', 'reshape2', 'ggplot2', 'viridis', 'gganimate',
  'vroom', 'tidyr', 'tibble', 'lubridate'

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', 'rvest', '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', 'car', 'haven', 'Hmisc', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'dplyr', 'ggplot2', 'AnnotationDbi', 'DESeq2', 'GEOquery',
  'stringr', 'ggnewscale', 'ggrepel', 'ggpattern', 'IRdisplay'

Packages suggested but not available for checking:
  'testthat', 'fgsea', 'CePa', 'meta', 'ggvenn', 'hgu133plus2.db',
  'org.Hs.eg.db', 'oligo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
File ‘RcppAlgos/libs/RcppAlgos.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
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RcppBDT.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘testthat’
File ‘RcppBigIntAlgos/libs/RcppBigIntAlgos.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
Specified C++11: please drop specification unless essential
Packages required but not available: 'ggplot2', 'StempCens'

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:
  > # 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: ‘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’
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
Specified C++11: please drop specification unless essential
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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/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-RcppHungarian.Rmd’ using rmarkdown

Quitting from lines 45-57 [unnamed-chunk-2] (Introduction-to-RcppHungarian.Rmd)
Error: processing vignette 'Introduction-to-RcppHungarian.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘Introduction-to-RcppHungarian.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-RcppHungarian.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking:
  'dplyr', 'testthat', '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
GNU make is a SystemRequirements.
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
Package required but not available: ‘nloptr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'devtools', '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’
checkRd: (-1) cSMCexamples.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
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:
  > Sys.setenv("OMP_THREAD_LIMIT" = 2)
  > 
  > 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("Rcpp")
  > library("RcppTN")
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Specified C++11: please drop specification unless essential
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
Package suggested but not available for checking: ‘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
Package required but not available: ‘selectr’

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:
  'forecast', 'ggmap', 'igraph', 'lubridate'

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', 'tibble', 'stringr'

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:
  'rms', 'ggplot2', 'survminer', 'dplyr', '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: ‘AER’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'purrr', 'tidyr', 'stringr', 'broom', 'forcats', '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:
  'ggplot2', 'ggpubr', 'PSweight', 'dplyr', 'geex', 'fastDummies',
  'tidyr', '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', 'purrr', 'stringr', 'tidyr', 'tibble', 'ggplot2', 'cellWise'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available:
  'dplyr', 'tibble', 'tidyselect', 'tidyr', 'purrr', 'stringr',
  'ggplot2', 'furrr'

Packages suggested but not available for checking: 'testthat', 'tcpl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Mercator’
Packages suggested but not available for checking:
  'readxl', 'ggplot2', 'tidyterra', 'stringr', 'rvest', 'testthat',
  'roxygen2', 'devtools', 'dplyr'
Running examples in ‘RCzechia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: KFME_grid
> ### Title: KFME grid cells (faunistické čtverce) of the Czech Republic
> ### Aliases: KFME_grid
> 
> ### ** 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
Note: skipping ‘vignette.Rmd’ due to unavailable dependencies: 'readxl'
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 required but not available: ‘roxygen2’

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.
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: 'configr', 'dplyr', 'usethis'

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', 'devtools', 'RSQLite', 'dbplyr', '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
'LazyData' is specified without a 'data' directory
Package required but not available: ‘AER’

Packages suggested but not available for checking:
  'devtools', 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'lpdensity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'ggplot2', 'rdd', 'rdrobust'

Packages suggested but not available for checking: 'car', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘run-testthat-rDEA.R’ [0s/0s]
Running the tests in ‘tests/run-testthat-rDEA.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: 'DiagrammeR', '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’
'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
Packages required but not available: 'redland', 'readr', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'purrr', 'lubridate', 'repurrrsive',
  'nycflights13'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'purrr', 'lubridate'

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 ‘RDHonest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RDScatter
> ### Title: Scatterplot of binned raw observations
> ### Aliases: RDScatter
> 
> ### ** Examples
> 
> RDScatter(log(earnings)~yearat14, data=cghs, cutoff=1947,
+                avg=Inf, propdotsize=TRUE)
Error: This function requires the ggplot2 package
Execution halted
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘RDHonest.Rmd’ using rmarkdown

Quitting from lines 83-89 [unnamed-chunk-2] (RDHonest.Rmd)
Error: processing vignette 'RDHonest.Rmd' failed with diagnostics:
This function requires the ggplot2 package
--- failed re-building ‘RDHonest.Rmd’

SUMMARY: processing the following file failed:
  ‘RDHonest.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘haven’

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:
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require(Rdiagnosislist)
  Loading required package: Rdiagnosislist
  
  Attaching package: 'Rdiagnosislist'
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, union
  
  > require(bit64)
  Loading required package: bit64
  Loading required package: bit
  
  Attaching package: 'bit'
  
  The following object is masked from 'package:base':
  
      xor
  
  Attaching package bit64
  package:bit64 (c) 2011-2017 Jens Oehlschlaegel
  creators: integer64 runif64 seq :
  coercion: as.integer64 as.vector as.logical as.integer as.double as.character as.bitstring
  logical operator: ! & | xor != == < <= >= >
  arithmetic operator: + - * / %/% %% ^
  math: sign abs sqrt log log2 log10
  math: floor ceiling trunc round
  querying: is.integer64 is.vector [is.atomic} [length] format print str
  values: is.na is.nan is.finite is.infinite
  aggregation: any all min max range sum prod
  cumulation: diff cummin cummax cumsum cumprod
  access: length<- [ [<- [[ [[<-
  combine: c rep cbind rbind as.data.frame
  WARNING don't use as subscripts
  WARNING semantics differ from integer
  for more help type ?bit64
  
  Attaching package: 'bit64'
  
  The following object is masked from 'package:utils':
  
      hashtab
  
  The following objects are masked from 'package:base':
  
      %in%, :, is.double, match, order, rank
  
  > require(data.table)
  Loading required package: data.table
  
  Attaching package: 'data.table'
  
  The following object is masked from 'package:bit':
  
      setattr
  
  > 
  > test_check("Rdiagnosislist")
  Error in test_check("Rdiagnosislist") : 
    could not find function "test_check"
  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
Specified C++11: please drop specification unless essential
checkRd: (-1) linear_RNDPROJ.Rd:45: Lost braces; missing escapes or markup?
    45 | there is a linear map \eqn{f:R^N} to {R^n} such that
       |                                      ^
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'devtools'
checkRd: (-1) halfnorm.like.Rd:105: Lost braces; missing escapes or markup?
   105 |   {f(x|a,b,c_1,c_2,...,c_k) = f(x|a,b)(1 + c(1) h_i1(x) + c(2) h_i2(x) + ... + c(k) h_ik(x)). }
       |   ^
checkRd: (-1) secondDeriv.Rd:15: Lost braces
    15 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) farthest_point_sampling.Rd:28: Lost braces; missing escapes or markup?
    28 | space P = {p_1, ..., p_k}, such that each p_i is the farthest 
       |           ^
'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: ‘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: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readxl', 'stringr', 'lubridate'

Packages suggested but not available for checking:
  'reshape2', 'dplyr', 'ggplot2', 'shinyMolBio', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'qad'
checkRd: (-1) computeCBMeasure.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:56: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'rdrobust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GOSemSim', 'org.Hs.eg.db'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cellWise’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'aws.alexa', 'devtools'

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: ‘devtools’

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: ‘rdrobust’

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', 'tibble', 'purrr', 'stringr', '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’

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:
  'ggplot2', 'network', 'igraph', 'reshape2', 'Hmisc', 'ergm'

Packages suggested but not available for checking: 'sspse', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'latex2exp'
Error(s) in re-building vignettes:
  ...
--- re-building ‘README.Rmd’ using rmarkdown

Quitting from lines 26-31 [setup] (README.Rmd)
Error: processing vignette 'README.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘README.Rmd’

SUMMARY: processing the following file failed:
  ‘README.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'roxygen2', 'testthat', 'vroom'
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'

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:
  'testthat', 'roxygen2', 'devtools', 'OSMscale', 'readr', 'gsheet'
Package required but not available: ‘stringr’

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:
  'mockery', 'shinytest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'stringr'

Package suggested but not available for checking: ‘dataui’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: '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
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: ‘usethis’
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'readxl', 'dplyr', 'purrr', 'tidyr', 'rvest', 'labelled'

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 ‘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
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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) reader-package.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:55: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
Packages suggested but not available for checking:
  'testthat', 'readr', 'lubridate'
Running examples in ‘read.gt3x-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gt3x_datapath
> ### Title: Path to read.gt3x package sample data
> ### Aliases: gt3x_datapath gt3x_filename
> 
> ### ** Examples
> 
> ## Not run: 
> ##D dir <- gt3x_datapath()
> ##D gt3x_filename <- gt3x_datapath(1)
> ##D stopifnot(!is.na(gt3x_datapath(2)))
> ## End(Not run)
> 
> testthat::expect_error(gt3x_filename(100))
Error in loadNamespace(x) : there is no package called ‘testthat’
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: 'haven', 'readr', 'readxl'

Packages suggested but not available for checking:
  'devtools', 'dplyr', '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: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) readMzXmlDir.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘testthat’
File ‘readNSx/libs/readNSx.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 ‘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
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: 'cellranger', 'tibble', 'vctrs'

Packages suggested but not available for checking: 'testthat', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rvest', 'purrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readxl', 'tidyr', 'dplyr', 'purrr', 'rvest', 'stringr', 'lubridate'

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: ‘qvalue’

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.
Packages required but not available: 'hms', 'tibble', 'vroom'

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’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'igraph', '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/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
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', 'purrr', 'readr', '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:
  'pillar', 'readODS', 'readxl', 'streamR', 'striprtf'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hms', 'RSQLite', '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', 'tibble', '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: ‘cellranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dataverse', 'dplyr', 'gh', 'kableExtra', 'piggyback', 'purrr',
  'rvest', 'stringr', 'tibble', 'tidyRSS', 'tidyselect'

Packages suggested but not available for checking:
  'devtools', 'Hmisc', 'readr', 'readxl', 'testthat', 'usethis',
  'zen4R'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'imputeTS', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'ggpubr', 'purrr', 'readxl', 'tidyr',
  'vcdExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'purrr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tidyr', 'xpectr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Automotive.Rd:29: Lost braces
    29 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). Own postprocessing.
       |                                                           ^
checkRd: (-1) Automotive.Rd:33: Lost braces
    33 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). 
       |                                                           ^
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: ‘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’
'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 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
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'purrr', 'tidyr', 'tibble', '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: ‘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', 'arrow', '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 suggested but not available for checking:
  'devtools', 'dplyr', '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: ‘lubridate’

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', 'clock', 'hardhat', 'lubridate', 'purrr', 'tibble', 'tidyr',
  'tidyselect', 'vctrs'

Packages suggested but not available for checking:
  'dials', 'ggplot2', 'igraph', 'modeldata', 'parsnip', 'rsample',
  'testthat', 'workflows'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phangorn', 'phytools'

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:
  > #R
  > 
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', '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
Packages required but not available: 'stringr', 'tidyr', 'haven', '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: ‘magick’
Running examples in ‘recogito-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ocv_crop_annotorious
> ### Title: Crop annotations to a bounding box
> ### Aliases: ocv_crop_annotorious
> 
> ### ** Examples
> 
> ## Don't show: 
> if(require(opencv))
+ {
+ ## End(Don't show)
+ library(opencv)
+ data(openseadragon_areas)
+ ## Don't show: 
+   url <- system.file(package = "recogito", "examples",
+                      "Cat_and_dog_standoff_(3926784260).jpg")
+   attr(openseadragon_areas, "src") <- url
+ ## End(Don't show)
+ url  <- attr(openseadragon_areas, "src")
+ img  <- ocv_read(url)
+ bbox <- ocv_info(img)
+ bbox <- c(xmin = 0, ymin = 0, xmax = bbox$width - 1, ymax = bbox$height - 1)
+ x    <- ocv_crop_annotorious(data = openseadragon_areas)
+ x    <- ocv_crop_annotorious(data = openseadragon_areas, bbox = bbox)
+ 
+ img
+ area <- x[2, ]
+ ocv_polygon(img, pts = area$polygon[[1]], crop = TRUE)
+ area <- x[1, ]
+ ocv_rectangle(img, x = area$x, y = area$y, width = area$width, height = area$height)
+ area <- x[3, ]
+ ocv_rectangle(img, x = area$x, y = area$y, width = area$width, height = area$height)
+ ## Don't show: 
+ }
Loading required package: opencv
Loading required namespace: magick
Failed with error:  ‘there is no package called ‘magick’’
Error in ocv_crop_annotorious(data = openseadragon_areas) : 
  Install packages magick to read the image or provide a bbox
Execution halted
Packages required but not available: 'imager', 'pavo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) recombinator.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) recombinator.Rd:35-38: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
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 suggested but not available for checking: 'kableExtra', '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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Evaluating_recommender_systems.Rmd’ using rmarkdown

Quitting from lines 265-279 [unnamed-chunk-3] (Evaluating_recommender_systems.Rmd)
Error: processing vignette 'Evaluating_recommender_systems.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘Evaluating_recommender_systems.Rmd’

SUMMARY: processing the following file failed:
  ‘Evaluating_recommender_systems.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: 'dplyr', 'ggplot2'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'survminer'

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: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'geepack', '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', 'prevR'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'readr', 'colourpicker'

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.
Packages suggested but not available for checking: 'car', 'UsingR'
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: ‘lubridate’

Packages suggested but not available for checking:
  'testthat', 'Hmisc', 'mockery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'REDCapR', 'tidyr', 'tidyselect', 'purrr', 'readr', 'haven',
  'readODS'

Packages suggested but not available for checking:
  'testthat', 'Hmisc', 'gt', 'ggplot2', 'styler', 'devtools',
  'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'janitor', 'purrr', 'REDCapR', 'stringr', 'tibble', 'tidyr',
  'tidyselect', 'labelled', 'forcats'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

Packages suggested but not available for checking:
  'devtools', 'qwraps2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'kableExtra', 'odbc', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'purrr', 'REDCapR', 'stringr', 'tibble',
  'tidyr', 'tidyselect', 'pillar', 'vctrs', 'readr'

Packages suggested but not available for checking:
  'labelled', 'skimr', '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 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
Package required but not available: ‘REddyProc’

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', 'tibble', 'solartime', 'bigleaf'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyr', 'tibble', 'lubridate'

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', 'kableExtra', 'magick', 'qvalue'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rediscover.Rmd’ using rmarkdown

Quitting from lines 21-30 [LoadFunctions] (Rediscover.Rmd)
Error: processing vignette 'Rediscover.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Rediscover.Rmd’

SUMMARY: processing the following file failed:
  ‘Rediscover.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'vctrs', 'dplyr'

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:
  'redistmetrics', 'vctrs', 'tidyselect', 'stringr', 'dplyr',
  'ggplot2', 'patchwork'

Packages suggested but not available for checking:
  'loo', 'rmapshaper', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

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: '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
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: 'BAT', 'gdistance'

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: ‘AER’
Running examples in ‘REEMtree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: REEMtree
> ### Title: Create a RE-EM tree
> ### Aliases: REEMtree
> ### Keywords: tree models
> 
> ### ** Examples
> 
> data(simpleREEMdata)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID)
> 
> # Estimation allowing for autocorrelation
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID,
+ 	correlation=corAR1())
> 
> # Random parameters model for the random effects
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1+X|ID)
> 
> # Estimation with a subset
> sub <- rep(c(rep(TRUE, 10), rep(FALSE, 2)), 50)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID,
+ 	subset=sub)
> 
> # Dataset from the R library "AER"
> data("Grunfeld", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Packages required but not available:
  'tibble', 'readr', 'dplyr', 'stringr', 'tidyr', 'taxize', 'bioseq',
  'igraph', 'ggplot2', 'ggraph'

Packages suggested but not available for checking: 'testthat', 'forcats'

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: ‘rcrossref’

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 ‘refinr-vignette.Rmd’ using rmarkdown

Quitting from lines 84-116 [unnamed-chunk-10] (refinr-vignette.Rmd)
Error: processing vignette 'refinr-vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘refinr-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘refinr-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'caret', 'dplyr'

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’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', '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: 'ggplot2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'lubridate', 'dplyr'

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 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: '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:
  'fda', 'gamm4', 'lme4', 'RLRsim', 'ggplot2'

Packages suggested but not available for checking: 'reshape2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'reshape2', 'dplyr', 'lme4', 'plotly', 'refund'

Packages suggested but not available for checking: 'testthat', 'registr'

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: 'dplyr', 'kableExtra', '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:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'lme4'

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', 'dtwclust'
Running ‘testthat.R’ [0s/1s]
Running 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:
  'dplyr', 'tidyselect', 'purrr', 'tidyr', 'readxl', 'stringr',
  'tibble'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'eurostat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'dplyr', 'gamm4', 'lme4', 'purrr'

Packages suggested but not available for checking:
  'testthat', 'cowplot', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'furrr', 'geepack', 'mice', 'modelr', 'purrr', 'stringr', 'testthat',
  'tidyverse', '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 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’
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: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom.helpers', 'dplyr'

Packages suggested but not available for checking:
  'roxygen2', 'see', '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:
  'broom', 'dplyr', 'ggplot2', 'nullabor', 'purrr', 'tibble', 'tidyr',
  'tidyselect'

Packages suggested but not available for checking: 'patchwork', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fbase1.binomial.Rd:32: Lost braces; missing escapes or markup?
    32 | In all base log-likelihood functions, we have dropped any additive terms that are independent of the distribution parameter, e.g. constant terms or those terms that are dependent on the response variable only. This is done for computational efficiency. Therefore, these functions cannot be used to obtain the absolute values of log-likelihood functions but only in the context of optimization and/or sampling. Users can write thin wrappers around these functions to add the constant terms to the function value. (Derivatives do not need correction. For binomial family, all factorial terms are ignored since they only depend on \code{n} and {y}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
Packages required but not available:
  'dplyr', 'loadeR', 'traineR', 'echarts4r'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'purrr', 'dplyr', 'tidyr', '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: ‘SSBtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'nloptr', 'optimx', 'semPlot', 'stringr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘short_intro.Rmd’ using knitr

Quitting from lines 45-46 [unnamed-chunk-3] (short_intro.Rmd)
Error: processing vignette 'short_intro.Rmd' failed with diagnostics:
there is no package called 'semPlot'
--- failed re-building ‘short_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘short_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'sjPlot', 'sjmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Packages suggested but not available for checking:
  'cdparcoord', 'keras', 'magick', 'partools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gap', 'testthat', 'vcfR'
checkRd: (-1) plot.ehh.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}} and \code{\link[graphics]{matplot}}). 
       |                                ^
checkRd: (-1) plot.ehhs.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}}.
       |                                ^
File ‘rehh/libs/rehh.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: 'rtweet', 'tibble', 'dplyr'

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/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: 'dplyr', 'viridis', 'ggplot2'

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
Error(s) in re-building vignettes:
  ...
--- re-building ‘restrictions.Rmd’ using rmarkdown

Quitting from lines 73-96 [many_to_many] (restrictions.Rmd)
Error: processing vignette 'restrictions.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building ‘restrictions.Rmd’

SUMMARY: processing the following file failed:
  ‘restrictions.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘densEstBayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EstimationTools’

Packages suggested but not available for checking: 'viridis', 'autoimage'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readxl', 'ggforce', 'ggplot2', 'dplyr'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'tidyr', 'ggplot2', 'ggExtra', 'dplyr', 'purrr', 'tibble', 'vctrs',
  'bde'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'PhaseType'

Packages suggested but not available for checking:
  'testthat', 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', '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: ‘Rcmdr’
Packages suggested but not available for checking: 'ggExtra', 'ggplot2'
Running examples in ‘relliptical-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rtelliptical
> ### Title: Sampling Random Numbers from Truncated Multivariate Elliptical
> ###   Distributions
> ### Aliases: rtelliptical
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
mvtelliptical 4.528   0.03   5.575
Packages required but not available: 'rvest', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'pammtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'EnvStats'

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 ‘Introduction_to_remap.Rmd’ using rmarkdown

Quitting from lines 26-35 [setup] (Introduction_to_remap.Rmd)
Error: processing vignette 'Introduction_to_remap.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Introduction_to_remap.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_to_remap.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘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: ‘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’
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 required but not available: ‘fda’

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: 'JointAI', 'ggplot2', 'mcmcse'

Packages suggested but not available for checking: 'ggpubr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geex’

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: ‘httr2’

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', 'sqldf', 'devtools', 'ggplot2', 'reshape2'
Running examples in ‘remotePARTS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fitAR_map
> ### Title: Map-level AR REML
> ### Aliases: fitAR_map
> 
> ### ** Examples
> 
> # simulate dummy data
>  time.points = 9 # time series length
>  map.width = 5 # square map width
>  coords = expand.grid(x = 1:map.width, y = 1:map.width) # coordinate matrix
>  ## create empty spatiotemporal variables:
>  X <- matrix(NA, nrow = nrow(coords), ncol = time.points) # response
>  Z <- matrix(NA, nrow = nrow(coords), ncol = time.points) # predictor
> # setup first time point:
>  Z[, 1] <- .05*coords[,"x"] + .2*coords[,"y"]
>  X[, 1] <- .5*Z[, 1] + rnorm(nrow(coords), 0, .05) #x at time t
>  ## project through time:
>  for(t in 2:time.points){
+    Z[, t] <- Z[, t-1] + rnorm(map.width^2)
+    X[, t] <- .2*X[, t-1] + .1*Z[, t] + .05*t + rnorm(nrow(coords), 0 , .25)
+  }
> 
> # visualize dummy data (NOT RUN)
> library(ggplot2);library(dplyr)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Alaska.Rmd’ using rmarkdown

Quitting from lines 41-43 [load_tidyverse] (Alaska.Rmd)
Error: processing vignette 'Alaska.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘Alaska.Rmd’

SUMMARY: processing the following file failed:
  ‘Alaska.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:
  > # 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’

Packages suggested but not available for checking:
  'ggplot2', 'see', 'ggrepel', 'ggsignif', 'qqplotr', 'broom',
  'ggpubr', 'interactions', 'patchwork', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'statnet', 'ggplot2'
Package suggested but not available for checking: ‘testthat’
Package suggested but not available for checking: ‘remify’
Running examples in ‘remstats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FEtype
> ### Title: FEtype
> ### Aliases: FEtype
> 
> ### ** Examples
> 
> history$type <- history$setting
> reh_tie <- remify::remify(history, model = "tie")
Error in loadNamespace(x) : there is no package called ‘remify’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘tinytest.R’ [1s/1s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  + 	tinytest::test_package("remstats")
  + }
  
  test-bind-remstats.R..........    0 tests    Error in loadNamespace(x) : there is no package called 'remify'
  Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘remstats.Rmd’ using rmarkdown

Quitting from lines 30-46 [unnamed-chunk-2] (remstats.Rmd)
Error: processing vignette 'remstats.Rmd' failed with diagnostics:
there is no package called 'remify'
--- failed re-building ‘remstats.Rmd’

SUMMARY: processing the following file failed:
  ‘remstats.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘remify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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: 'optimx', 'AER', '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’
checkRd: (-1) rentrez.Rd:17-21: Lost braces
    17 | /enumerated{
       |            ^
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 ‘rentrez_tutorial.Rmd’ using rmarkdown

Quitting from lines 15-28 [count_recs] (rentrez_tutorial.Rmd)
Error: processing vignette 'rentrez_tutorial.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building ‘rentrez_tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘rentrez_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'devtools', 'testthat', '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
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', 'lubridate', 'readr'

Packages suggested but not available for checking:
  'testthat', 'RSQLite', 'RPostgres', 'targets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'netmeta', 'progress'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'stringr'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'reshape2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) twosidedPValuestobins.Rd:84: Lost braces; missing escapes or markup?
    84 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
checkRd: (-1) ztobins.Rd:90: Lost braces; missing escapes or markup?
    90 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
Packages suggested but not available for checking: 'kableExtra', 'testthat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘readmefirst.Rmd’ using rmarkdown

Quitting from lines 125-132 [tables] (readmefirst.Rmd)
Error: processing vignette 'readmefirst.Rmd' failed with diagnostics:
could not find function "kable_styling"
--- failed re-building ‘readmefirst.Rmd’

SUMMARY: processing the following file failed:
  ‘readmefirst.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dat’

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', 'lmerTest', 'pbkrtest'

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: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'roxygen2', '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: 'ggplot2', 'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘PackageCites.bib’
Packages required but not available: 'lme4', 'lmerTest'

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: 'igraph', 'testthat'
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
checkRd: (-1) repo_dependencies.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
Running examples in ‘repo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: repo_dependencies
> ### Title: Build and/or plots a dependency graph
> ### Aliases: repo_dependencies
> 
> ### ** Examples
> 
> ## Repository creation
> rp_path <- file.path(tempdir(), "example_repo")
> rp <- repo_open(rp_path, TRUE)
Repo root created.
Repo created.
> 
> ## Producing some irrelevant data
> data1 <- 1:10
> data2 <- data1 * 2
> data3 <- data1 + data2
> 
> ## Putting the data in the database, specifying dependencies
> rp$put(data1, "item1", "First item",
+     "repo_dependencies")
> rp$put(data2, "item2", "Item dependent on item1", 
+     "repo_dependencies", depends="item1")
> rp$put(data3, "item3", "Item dependent on item1 and item2",
+     "repo_dependencies", depends=c("item1", "item2"))
> 
> ## Creating a temporary plot and attaching it
> fpath <- file.path(rp$root(), "temp.pdf")
> pdf(fpath)
> plot(data1)
> dev.off()
pdf 
  2 
> rp$attach(fpath, "visualization of item1", "plot",
+    to="item1")
> 
> ## Obtaining the dependency matrix
> depmat <- rp$dependencies(plot=FALSE)
> print(depmat)
         item1 item2 item3 temp.pdf
item1        0     0     0        0
item2        1     0     0        0
item3        1     1     0        0
temp.pdf     2     0     0        0
> ## The matrix can be plotted as a graph (requires igraph package)
> rp$dependencies()
Error in rp$dependencies() : 
  The suggested package igraph is not installed.
Execution halted