Packages required but not available: 'lamW', 'readxl'

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

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

> ### Name: tz_plot
> ### Title: Plot a time zone
> ### Aliases: tz_plot
> 
> ### ** Examples
> 
> tz_plot("America/Vancouver")
Error in tz_plot("America/Vancouver") : ggplot2 rquired
Execution halted
Packages required but not available: 'torch', 'cli'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'tests.R'
Running the tests in 'tests/tests.R' failed.
Complete output:
  > library(lvec)
  
  Attaching package: 'lvec'
  
  The following object is masked from 'package:base':
  
      order
  
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'cowplot', 'dplyr', 'ggplot2', 'rsample', 'tibble'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'gWQS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  lxb.c:62:25: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  lxb.c:62:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 4 [-Wformat-overflow=]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/lxb/lxb.Rcheck/00install.out' for details.
Packages required but not available: 'ggplot2', 'caret'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mpoly', '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:
  'GenomicAlignments', 'GenomicFeatures', 'Rsamtools'

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

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

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

Packages suggested but not available for checking:
  'adabag', 'Hmisc', 'kableExtra', 'randomForestSRC', 'rms', 'testthat'

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

Packages suggested but not available for checking:
  'ggplot2', 'dbplyr', 'broom', 'leaflet', 'clifro', 'testthat'

VignetteBuilder packages required for checking but not installed:
  'etl', 'dplyr', 'ggplot2', 'leaflet', 'clifro'

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

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.
Error(s) in re-building vignettes:
--- re-building 'maddison_project_database.Rmd' using rmarkdown
Quitting from lines 33-38 (maddison_project_database.Rmd) 
Error: processing vignette 'maddison_project_database.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'maddison_project_database.Rmd'

SUMMARY: processing the following file failed:
  'maddison_project_database.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'torch'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # /usr/bin/r
  > #
  > # Copyright 2015-2015 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > #
  > # This file is part of madness.
  > #
  > # madness is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU Lesser General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # madness is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU Lesser General Public License for more details.
  > #
  > # You should have received a copy of the GNU Lesser General Public License
  > # along with madness.  If not, see <http://www.gnu.org/licenses/>.
  > #
  > # Created: 2015.11.28
  > # Copyright: Steven E. Pav, 2015
  > # Author: Steven E. Pav <shabbychef@gmail.com>
  > # Comments: Steven E. Pav
  > 
  > # because Hadley says it should be like this.
  > # see https://github.com/hadley/devtools/wiki/Testing
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'introducing_madness.Rnw' using knitr
Quitting from lines 1148-1202 (introducing_madness.Rnw) 
Error: processing vignette 'introducing_madness.Rnw' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'introducing_madness.Rnw'

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

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

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'MAd-Ex.R' failed
The error most likely occurred in:

> ### Name: plotcon
> ### Title: Meta Regression Scatterplot
> ### Aliases: plotcon
> ### Keywords: aplot
> 
> ### ** Examples
> 
> # SAMPLE DATA
> MA2 <-read.table(textConnection("
+ id       es1       var1 n.1 n.2 mod1 mod2
+ 1   1 0.5695938 0.04906967  26  30    a   20
+ 2   2 0.4123667 0.04362541  28  34    b   30
+ 3   3 0.4084333 0.04458363  34  28    a   25
+ 4   4 0.5014756 0.04186354  37  29    b   35
+ 5   5 0.5540745 0.04339382  31  32    b   40
+ 6   1 0.5695938 0.04906967  26  30    a   20
+ 7   2 0.4123667 0.04362541  28  34    b   30
+ 8   3 0.4084333 0.04458363  34  28    a   25
+ 9   4 0.5014756 0.04186354  37  29    b   35
+ 10  5 0.5540745 0.04339382  31  32    b   40"))
> 
> 
> # EXAMPLE
> plotcon(es1, var1, mod2, data=MA2, method= "fixed", modname="NULL",title="NULL")
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Loading required package: metafor
Loading required package: Matrix

Loading the 'metafor' package (version 3.0-2). For an
introduction to the package please type: help(metafor)

Warning in model.matrix.default(terms, mf, contrasts) :
  non-list contrasts argument ignored
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: plotcon ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'test-that.R'
Running the tests in 'tests/test-that.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'TCGAbiolinks', 'plotly', 'dplyr', 'ggbeeswarm'

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

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

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

> ### Name: device
> ### Title: Magick Graphics Device
> ### Aliases: device image_graph image_device image_draw image_capture
> 
> ### ** Examples
> 
> # Regular image
> frink <- image_read("https://jeroen.github.io/images/frink.png")
> 
> # Produce image using graphics device
> fig <- image_graph(res = 96)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = cyl)
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'intro.Rmd' using rmarkdown
Linking to librsvg 2.48.8
Using poppler version 21.04.0
Quitting from lines 415-419 (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 suggested but not available for checking: 'dittoSeq', 'testthat'
Packages suggested but not available for checking:
  'GEOquery', 'GEOmetadb', 'WGCNA', 'lumi', 'simpleaffy', 'beadarray'
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 required but not available:
  'gmailr', 'googledrive', 'dplyr', 'googlesheets4'

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

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

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

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

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: '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: 'readr', 'dplyr', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'leaflet', 'plotly', 'testthat'
Package unavailable to check Rd xrefs: 'leaflet'
Packages suggested but not available for checking:
  'tidyr', 'ggplot2', 'testthat'
Running examples in 'MANOVA.RM-Ex.R' failed
The error most likely occurred in:

> ### Name: EEG
> ### Title: EEG Measurements in Patients with Alzheimer's Disease (long
> ###   format)
> ### Aliases: EEG
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_MANOVA.RM.Rmd' using rmarkdown
Quitting from lines 352-357 (Introduction_to_MANOVA.RM.Rmd) 
Error: processing vignette 'Introduction_to_MANOVA.RM.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'Introduction_to_MANOVA.RM.Rmd'

SUMMARY: processing the following file failed:
  'Introduction_to_MANOVA.RM.Rmd'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'gtools' 'reshape'
  All declared Imports should be used.
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', 'tibble', 'tidyr'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'leafem', 'leaflet', 'leaflet.extras', 'leafpm', 'mapview',
  'sf'

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

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

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

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tmap', 'cartography', 'ggplot2', 'sf', 'dplyr', 'leaflet',
  'tmaptools', 'leafpop', 'leafsync', 'mapview', 'geojsonio'

Package suggested but not available for checking: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'fields', 'ggpubr', 'ggsci', 'dplyr', 'cli', 'ggplot2', 'smacof',
  'dendextend', 'vcfR', 'plotly'

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

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

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

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

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

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

Package suggested but not available for checking: 'lwgeom'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rnaturalearth'
Packages required but not available: 'leafem', 'leaflet', 'leafpop', 'sf'

Packages suggested but not available for checking:
  'leaflet.extras2', 'leafsync', 'lwgeom', 'stars'

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

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

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', 'gapminder'

Package which this enhances but not available for checking: 'AER'
Running 'testthat-margins.R'
Running the tests in 'tests/testthat-margins.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 356-364 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Introduction.Rmd'

--- re-building 'Stata.Rmd' using rmarkdown
--- finished re-building 'Stata.Rmd'

--- re-building 'TechnicalDetails.Rnw' using knitr
  ordinary text without R code

label: model1 (with options) 
List of 1
 $ results: chr "asis"

   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ R code chunk ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
   library("gapminder")
   suppressPackageStartupMessages(library("stargazer"))
   gapminder[["pop"]] <- gapminder[["pop"]]/1e6
   gapminder[["loggdp"]] <- log(gapminder[["gdpPercap"]])
   m1 <- lm(pop ~ loggdp + lifeExp, data = gapminder)
   m2 <- lm(pop ~ loggdp * lifeExp, data = gapminder)
   stargazer(m1, m2, dep.var.labels = "Population Size",
             title = "Example OLS Regression Output", 
             label = "tab:model1") 
   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
##------ Wed Aug  4 23:56:41 2021 ------##

Quitting from lines 45-54 (TechnicalDetails.Rnw) 
Error: processing vignette 'TechnicalDetails.Rnw' failed with diagnostics:
there is no package called 'gapminder'
--- failed re-building 'TechnicalDetails.Rnw'

SUMMARY: processing the following files failed:
  'Introduction.Rmd' 'TechnicalDetails.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'kableExtra'

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', '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: 'RcppParallel'

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'

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

Packages suggested but not available for checking:
  'bench', 'bib2df', 'dplyr', 'rcmdcheck', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'viridis', 'patchwork'
Error(s) in re-building vignettes:
--- re-building 'mla.Rmd' using rmarkdown
Quitting from lines 149-154 (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
Packages suggested but not available for checking:
  'broom', 'forecast', 'ggplot2', 'Hmisc', 'tidyr', 'testthat'
Running examples in 'MARSS-Ex.R' failed
The error most likely occurred in:

> ### Name: accuracy.marssMLE
> ### Title: Return accuracy metrics
> ### Aliases: accuracy.marssMLE accuracy.marssPredict
> 
> ### ** Examples
> 
> dat <- t(harborSeal)
> dat <- dat[c(2, 11, 12),]
> train.dat <- dat[,1:12]
> fit <- MARSS(train.dat, model = list(Z = factor(c("WA", "OR", "OR"))))
Success! abstol and log-log tests passed at 79 iterations.
Alert: conv.test.slope.tol is 0.5.
Test with smaller values (<0.1) to ensure convergence.

MARSS fit is
Estimation method: kem 
Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
Estimation converged in 79 iterations. 
Log-likelihood: 14.98234 
AIC: -13.96467   AICc: -2.887748   
 
                Estimate
A.OR.SouthCoast   0.8952
R.diag            0.0087
U.WA              0.1043
U.OR              0.0569
Q.(WA,WA)         0.0112
Q.(OR,OR)         0.0000
x0.WA             7.3171
x0.OR             6.2970
Initial states (x0) defined at t=0

Standard errors have not been calculated. 
Use MARSSparamCIs to compute CIs and bias estimates.

> 
> library(forecast)
Error in library(forecast) : there is no package called 'forecast'
Execution halted
Packages required but not available:
  'dplyr', 'FactoMineR', 'factoextra', 'ggplot2', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'forestinventory', 'pkgload', 'testthat'
Package unavailable to check Rd xrefs: 'forestinventory'
Package required but not available: 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'flashr'
Packages required but not available: 'broom', 'dplyr', 'tibble', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'patchwork', 'tidyverse'
Error(s) in re-building vignettes:
--- re-building 'rationale.Rmd' using rmarkdown
Quitting from lines 19-32 (rationale.Rmd) 
Error: processing vignette 'rationale.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'rationale.Rmd'

SUMMARY: processing the following file failed:
  'rationale.Rmd'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'matching.Rnw' using knitr_notangle
Quitting from lines 65-75 (././Sections/4_MonteCarloResults.Rnw) 
Quitting from lines 39-40 (././Sections/4_MonteCarloResults.Rnw) 
Error: processing vignette 'matching.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'matching.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'cobalt'
Package unavailable to check Rd xrefs: 'cobalt'
Error(s) in re-building vignettes:
--- re-building 'MatchIt.Rmd' using rmarkdown
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

--- finished re-building 'MatchIt.Rmd'

--- re-building 'assessing-balance.Rmd' using rmarkdown
Quitting from lines 224-225 (assessing-balance.Rmd) 
Error: processing vignette 'assessing-balance.Rmd' failed with diagnostics:
there is no package called 'cobalt'
--- failed re-building 'assessing-balance.Rmd'

--- re-building 'estimating-effects.Rmd' using rmarkdown

Attaching package: 'survival'

The following object is masked from 'package:boot':

    aml

--- finished re-building 'estimating-effects.Rmd'

--- re-building 'matching-methods.Rmd' using rmarkdown
--- finished re-building 'matching-methods.Rmd'

--- re-building 'sampling-weights.Rmd' using rmarkdown
--- finished re-building 'sampling-weights.Rmd'

SUMMARY: processing the following file failed:
  'assessing-balance.Rmd'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'cobalt'

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

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', 'tidyverse', 'plotly', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'spelling.R'
  Comparing 'spelling.Rout' to 'spelling.Rout.save' ... OK
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction-to-matrixnormal-package.Rmd' using rmarkdown
Quitting from lines 168-177 (introduction-to-matrixnormal-package.Rmd) 
Error: processing vignette 'introduction-to-matrixnormal-package.Rmd' failed with diagnostics:
there is no package called 'sessioninfo'
--- failed re-building 'introduction-to-matrixnormal-package.Rmd'

SUMMARY: processing the following file failed:
  'introduction-to-matrixnormal-package.Rmd'

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: 'sem'
Package which this enhances but not available for checking: 'spdep'
Packages suggested but not available for checking:
  'testthat', 'car', 'cosinor', 'cosinor2'
Packages unavailable to check Rd xrefs: 'cosinor', 'car'
Packages required but not available: 'dplyr', 'Hmisc', 'tibble'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'maxLik-Ex.R' failed
The error most likely occurred in:

> ### 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
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Packages required but not available: 'devtools', 'dplyr', 'tibble', 'rvest'

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', 'MazamaSpatialUtils', 'readr'

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', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
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
Packages suggested but not available for checking: 'emojifont', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'inspiration.Rmd' using rmarkdown
Quitting from lines 123-130 (inspiration.Rmd) 
Error: processing vignette 'inspiration.Rmd' failed with diagnostics:
could not find function "emoji"
--- failed re-building 'inspiration.Rmd'

SUMMARY: processing the following file failed:
  'inspiration.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'check-formula-integral.R'
  Running 'check-formula-variance.R'
  Running 'test-1inf-GB1.R'
  Running 'test-1inf-beta.R'
  Running 'test-1inf-mean.R'
  Running 'test-1inf-shftrncPareto.R'
  Running 'test-1inf-unif.R'
  Running 'test-GB1.R'
  Running 'test-asiacom.R'
  Running 'test-beaonre.R'
  Running 'test-beta.R'
  Running 'test-eecf.R'
  Running 'test-fit-MBBEFDgb.R'
  Running 'test-fit-gbeta.R'
  Running 'test-fit-mbbefd.R'
  Running 'test-fit-oibeta.R'
  Running 'test-fit-oigbeta.R'
  Running 'test-fit-oistpareto.R'
  Running 'test-fit-oiunif.R'
  Running 'test-lossalae.R'
  Running 'test-mbbefd-1stparam.R'
  Running 'test-mbbefd-2ndparam.R'
  Running 'test-rng-mbbefd.R'
  Running 'test-shftrncPareto.R'
  Running 'test-smokedfish.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'OpenMx', 'sem'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'logistf'
Packages suggested but not available for checking: 'fields', 'spsurvey'
Error(s) in re-building vignettes:
--- re-building 'MBHdesign.Rnw' using knitr
Quitting from lines 198-211 (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
Namespaces in Imports field not imported from:
  'effsize' 'psych'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'MBmca.Rmd' using rmarkdown
! Missing $ inserted.
<inserted text> 
                $
l.167 ...ed to Bendamustine by an Automated \gamma
                                                  {H}2ax Assay---an 

! pdflatex: major issue: User/administrator updates are out-of-sync.

Try to find the following text in C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/MBmca/MBmca.Rcheck/vign_test/MBmca/vignettes/MBmca.Rmd:
  ...ed to Bendamustine by an Automated \gamma 

You may need to add $ $ around a certain inline R expression `r ` in C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/MBmca/MBmca.Rcheck/vign_test/MBmca/vignettes/MBmca.Rmd (see the above hint). See https://github.com/rstudio/rmarkdown/issues/385 for more info.
Error: processing vignette 'MBmca.Rmd' failed with diagnostics:
LaTeX failed to compile C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/MBmca/MBmca.Rcheck/vign_test/MBmca/vignettes/MBmca.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MBmca.log for more info.
--- failed re-building 'MBmca.Rmd'

SUMMARY: processing the following file failed:
  'MBmca.Rmd'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'fields', 'testthat', 'kangar00'
Packages unavailable to check Rd xrefs: 'fields', 'kangar00'
Packages required but not available: 'cowplot', 'dplyr', 'ggplot2', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'boot.heterogeneity'
  All declared Imports should be used.
Package required but not available: 'memisc'

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

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

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

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'
Error(s) in re-building vignettes:
--- re-building 'diagnostic-pkgs.Rmd' using rmarkdown
Quitting from lines 85-86 (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
--- 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: 'nlist'

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:
  'spdep', 'bayesplot', 'testthat', 'roxygen2'
Packages required but not available: 'rstan', '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: 'ecr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'devtools', 'roxygen2', 'testthat', 'gh', 'pkgbuild',
  'VIM', 'FactoMineR', 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'mdendro-Ex.R' failed
The error most likely occurred in:

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

      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
Error(s) in re-building vignettes:
--- re-building 'mdendro-vignette.Rmd' using rmarkdown
Quitting from lines 171-188 (mdendro-vignette.Rmd) 
Error: processing vignette 'mdendro-vignette.Rmd' failed with diagnostics:
there is no package called 'dendextend'
--- failed re-building 'mdendro-vignette.Rmd'

SUMMARY: processing the following file failed:
  'mdendro-vignette.Rmd'

Error: Vignette re-building failed.
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 required but not available:
  'leaflet', 'leaflet.extras', 'ggplot2', 'dplyr', 'readxl', 'plotly'

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

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

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

Package suggested but not available for checking: 'testthat'

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

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', 'skimr',
  'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cowplot', 'hrbrthemes', 'ggplot2', 'ggtext', 'ggthemes', 'tvthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'MethylCapSig'
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.
Error(s) in re-building vignettes:
--- re-building 'mxr_basic_vignette.Rmd' using rmarkdown
Quitting from lines 15-17 (mxr_basic_vignette.Rmd) 
Error: processing vignette 'mxr_basic_vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'mxr_basic_vignette.Rmd'

--- re-building 'mxr_tapering_vignette.Rmd' using rmarkdown
--- finished re-building 'mxr_tapering_vignette.Rmd'

SUMMARY: processing the following file failed:
  'mxr_basic_vignette.Rmd'

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

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.
Error(s) in re-building vignettes:
--- re-building 'advanced.Rmd' using rmarkdown
Quitting from lines 50-60 (advanced.Rmd) 
Error: processing vignette 'advanced.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'advanced.Rmd'

--- re-building 'medicalrisk.Rmd' using rmarkdown
--- finished re-building 'medicalrisk.Rmd'

SUMMARY: processing the following file failed:
  'advanced.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'cost-report-analysis.Rmd' using rmarkdown
Quitting from lines 61-67 (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
Packages required but not available: 'ggplot2', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'vroom', 'bib2df', 'tibble'

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

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

Package suggested but not available for checking: 'klaR'

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

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

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

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', 'ggimage', 'shadowtext'

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

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: 'adegenet'
Running examples in 'memgene-Ex.R' failed
The error most likely occurred in:

> ### Name: codomToPropShared
> ### Title: Find proportion of shared alleles genetic distances from a
> ###   codominant alleles matrix
> ### Aliases: codomToPropShared
> 
> ### ** Examples
> 
> 
> radialData <- read.csv(system.file("extdata/radial.csv", package="memgene"))
> radialGen <- radialData[, -c(1,2)]
> radialDM <- codomToPropShared(radialGen)
Loading required package: adegenet
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'adegenet'
Error: memgene:  Please install the adegenet package to find the proportion of shared alleles
Execution halted
Error(s) in re-building vignettes:
--- re-building 'memgeneTutorial.Rnw' using knitr
Quitting from lines 21-30 (memgeneTutorial.Rnw) 
Error: processing vignette 'memgeneTutorial.Rnw' failed with diagnostics:
there is no package called 'adegenet'
--- failed re-building 'memgeneTutorial.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'repr'

Packages which this enhances but not available for checking:
  'AER', 'car', 'tibble', 'haven'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'googleAuthR', 'googleCloudStorageR', 'testthat'
Packages required but not available:
  'ggplot2', 'cowplot', 'viridis', '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', 'EnvStats'

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.
Package required but not available: 'randomizeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
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:
  'arm', 'dplyr', 'ggplot2', '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: 'geepack', 'ggplot2', 'ggformula'

Package suggested but not available for checking: 'testthat'

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'usethis', 'dplyr', 'ggplot2', 'ggfittext', 'cli',
  'forcats', 'ggimage', 'patchwork', 'tidyr'

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'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rvest', 'WikidataQueryServiceR', 'webchem', 'ChemmineR', 'Hmisc',
  'readxl'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'Epi', 'testthat'
Running 'testthat.R'
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', 'ggplot2', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Packages required but not available:
  'ggplot2', 'GEOquery', 'GEOmetadb', 'ggpubr', 'manhattanly', 'dplyr',
  'readr', 'plotly'

Package suggested but not available for checking: 'snplist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dataone', 'dplyr', 'EML', 'readr', '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', 'DESeq2'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'GGally', 'ggforce', 'ggplot2', 'ggrepel', 'lmerTest',
  'patchwork', 'tibble', 'tidyr'

Package suggested but not available for checking: 'roxygen2'

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.
Packages required but not available:
  'dendextend', 'dplyr', 'ggforce', 'ggrepel', 'tidyverse'

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

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

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

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', 'nullabor', 'dplyr', 'ggpubr'

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

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: 'spdep'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'metricsgraphics-Ex.R' failed
The error most likely occurred in:

> ### Name: mjs_add_confidence_band
> ### Title: Add a confidence band to line plot
> ### Aliases: mjs_add_confidence_band
> 
> ### ** Examples
> 
> require(binom)
Loading required package: binom
> require(dplyr)
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'dplyr'
> 
> set.seed(1492)
> binom.confint(x=sample(2:30, 100, replace=TRUE), n = 100, tol = 1e-8,
+               methods="bayes") %>%
+   mutate(x=1:100) -> bdat
Error in mutate(., x = 1:100) : could not find function "mutate"
Calls: %>%
Execution halted
Error(s) in re-building vignettes:
--- re-building 'MetricsWeighted.Rmd' using rmarkdown
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'dplyr'
Quitting from lines 167-214 (MetricsWeighted.Rmd) 
Error: processing vignette 'MetricsWeighted.Rmd' failed with diagnostics:
could not find function "%>%"
--- failed re-building 'MetricsWeighted.Rmd'

SUMMARY: processing the following file failed:
  'MetricsWeighted.Rmd'

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

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

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

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', 'cowplot'
Error(s) in re-building vignettes:
--- re-building 'basic-dutils.Rmd' using rmarkdown
--- finished re-building 'basic-dutils.Rmd'

--- re-building 'binomial-family.Rmd' using rmarkdown
--- finished re-building 'binomial-family.Rmd'

--- re-building 'binomial-twin.Rmd' using rmarkdown
--- finished re-building 'binomial-twin.Rmd'

--- re-building 'cifreg.Rmd' using rmarkdown
--- finished re-building 'cifreg.Rmd'

--- re-building 'haplo-discrete-ttp.Rmd' using rmarkdown
--- finished re-building 'haplo-discrete-ttp.Rmd'

--- re-building 'marginal-cox.Rmd' using rmarkdown
--- finished re-building 'marginal-cox.Rmd'

--- re-building 'quantitative-twin.Rmd' using rmarkdown
Quitting from lines 79-105 (quantitative-twin.Rmd) 
Error: processing vignette 'quantitative-twin.Rmd' failed with diagnostics:
there is no package called 'cowplot'
--- failed re-building 'quantitative-twin.Rmd'

--- re-building 'recurrent-events.Rmd' using rmarkdown
--- finished re-building 'recurrent-events.Rmd'

--- re-building 'twostage-survival.Rmd' using rmarkdown
--- finished re-building 'twostage-survival.Rmd'

SUMMARY: processing the following file failed:
  'quantitative-twin.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'revdbayes'
Packages required but not available:
  'ggplot2', 'RcppParallel', 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'ggridges', 'alfred'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'dplyr', 'dbplyr'
Namespace in Imports field not imported from: 'ECoL'
  All declared Imports should be used.
Packages suggested but not available for checking: 'tsDyn', 'forecast'
Package suggested but not available for checking: 'dataRetrieval'
Namespaces in Imports field not imported from:
  'boot' 'energy'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'Discriminability.Rmd' using rmarkdown
Quitting from lines 17-33 (Discriminability.Rmd) 
Error: processing vignette 'Discriminability.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Discriminability.Rmd'

--- re-building 'MGC.Rmd' using rmarkdown
Quitting from lines 13-50 (MGC.Rmd) 
Error: processing vignette 'MGC.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'MGC.Rmd'

--- re-building 'class_simulations.Rmd' using rmarkdown
Loading required package: ggplot2
Quitting from lines 40-42 (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
Loading required package: ggplot2
Quitting from lines 64-69 (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', 'viridis', 'GGally'

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', 'qgraph'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MCMCpack' 'copula'
  All declared Imports should be used.
Package required but not available: 'mice'

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

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

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.
Packages suggested but not available for checking: 'Ecdat', 'systemfit'
Packages unavailable to check Rd xrefs: 'micEconAids', 'micEconSNQP'
Packages required but not available: 'dplyr', 'UpSetR', 'ggplot2', 'tidyr'

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

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

Package suggested but not available for checking: 'VIM'

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

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

Packages suggested but not available for checking:
  'broom.mixed', 'haven', 'mitml', 'miceadds', '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'
Package unavailable to check Rd xrefs: 'MVN'
Running examples in 'micompr-Ex.R' failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright (c) 2016 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'paper.Rnw' using knitr
Quitting from lines 341-342 (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
Warning in wilcox.test.default(x = c(-2.17390550005803e-11, -2.17097451127302e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(2.13309370167281e-11, 2.12594386539422e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.99236183107132e-11, 1.97388771994156e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.00897068477934e-12, 1.02406971791424e-12,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(8.95727936267576e-13, 8.4909856923332e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.80548975348938e-13, 8.81072992342524e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(5.90887339058099e-11, 6.09077233093558e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.97119053991469e-15, 9.92695509127728e-15,  :
  cannot compute exact p-value with ties
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'tolatex-examples.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'broom', 'phyloseq', 'ggplot2', 'ggpubr', 'DESeq2', 'dada2',
  'rstatix', 'tidyr', 'testthat'

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

Packages suggested but not available for checking:
  'ggpubr', 'ggdendro', 'ggrepel', 'agricolae', 'tidytree', 'mice',
  'ggtree'

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.
Packages required but not available: 'microseq', 'dplyr', 'tibble'

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

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

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

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

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10'

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', 'usethis', 'httptest', 'pkgload'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'blastula'
Namespaces in Imports field not imported from:
  'AzureAuth' 'R6' 'curl' 'jsonlite' 'vctrs'
  All declared Imports should be used.
Running examples in 'midastouch-Ex.R' failed
The error most likely occurred in:

> ### Name: mice.impute.midastouch
> ### Title: Predictive Mean Matching with distance aided selection of donors
> ### Aliases: mice.impute.midastouch midastouch
> ### Keywords: mice
> 
> ### ** Examples
> 
> ## from R:: mice, slightly adapted ##
> 
> # do default multiple imputation on a numeric matrix
> library(midastouch)
> library(mice)
Error in library(mice) : there is no package called 'mice'
Execution halted
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.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'forcats', 'ggplot2'

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

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: 'mi', 'arm'

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:
  'ggplot2', 'testthat', 'tidyr'

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

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

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

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

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: 'kableExtra'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'testthat', 'mockery', 'testthis', 'roxygen2'
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tidyr', 'tibble'
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 128-161 (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
Namespaces in Imports field not imported from:
  'DiceDesign' 'MaxPro' 'doSNOW' 'gmp' 'jpeg'
  All declared Imports should be used.
Packages required but not available: 'colourpicker', 'readxl'

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

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:
  'rstan', 'rstantools', 'dirichletprocess', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'plotly', 'readr', 'readxl', 'tidyr',
  'tidytext'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'propr', 'tidyverse', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'MiRKAT_Vignette.Rmd' using rmarkdown
This is vegan 2.5-7
Quitting from lines 19-25 (MiRKAT_Vignette.Rmd) 
Error: processing vignette 'MiRKAT_Vignette.Rmd' failed with diagnostics:
there is no package called 'propr'
--- failed re-building 'MiRKAT_Vignette.Rmd'

SUMMARY: processing the following file failed:
  'MiRKAT_Vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'SimDesign'
Package required but not available: 'GlobalAncova'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'misaem.Rmd' using rmarkdown
Quitting from lines 60-68 (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
Packages required but not available: 'devtools', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'miscTools-Ex.R' failed
The error most likely occurred in:

> ### 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'
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
Error(s) in re-building vignettes:
--- re-building 'miselect.Rmd' using rmarkdown
Quitting from lines 76-82 (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
Package required but not available: 'aSPU'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'list'
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:
  'ggpubr', 'ggmcmc', 'ggthemes', 'BCEA', 'ggplot2', 'bayesplot',
  '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'
Error(s) in re-building vignettes:
--- re-building 'Generating-missing-values.Rmd' using rmarkdown
Quitting from lines 52-65 (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
Error(s) in re-building vignettes:
--- re-building 'censored_variables.Rmd' using rmarkdown
Quitting from lines 49-82 (censored_variables.Rmd) 
Error: processing vignette 'censored_variables.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building 'censored_variables.Rmd'

--- re-building 'missRanger.Rmd' using rmarkdown
Quitting from lines 63-76 (missRanger.Rmd) 
Error: processing vignette 'missRanger.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'missRanger.Rmd'

--- re-building 'multiple_imputation.Rmd' using rmarkdown
Quitting from lines 34-53 (multiple_imputation.Rmd) 
Error: processing vignette 'multiple_imputation.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building 'multiple_imputation.Rmd'

SUMMARY: processing the following files failed:
  'censored_variables.Rmd' 'missRanger.Rmd' 'multiple_imputation.Rmd'

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

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:
  'car', 'ggplot2', 'fdapace'
Running examples in 'mistr-Ex.R' failed
The error most likely occurred in:

> ### 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

Attaching package: 'mistr'

The following object is masked from 'package:base':

    q

Quitting from lines 180-184 (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
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
Quitting from lines 212-214 (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: 'haven', 'readxl'

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

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

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

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

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:

> ### 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
Package required but not available: 'kdensity'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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 (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
--- finished re-building 'mixturemodel.Rmd'

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

Error: Vignette re-building failed.
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.
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.
Packages required but not available: 'ggplot2', 'ggmcmc', 'bayesplot'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'ashr' 'fdrtool'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'ggplot2', 'plotly'

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: 'MKdescr', 'ggplot2'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
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
Package unavailable to check Rd xrefs: 'MKmisc'
Packages required but not available:
  'ggplot2', 'MKdescr', 'MKinfer', 'qqplotr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Matrix' 'R6'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'janitor', 'rvest'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ergm', 'network', 'GGally', 'ggplot2', 'cowplot', 'sna'

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

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

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

Packages suggested but not available for checking:
  'lintr', 'mleap', 'sparklyr', 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
Packages suggested but not available for checking: 'bootImpute', 'testthat'
Packages suggested but not available for checking:
  'minfi', 'GEOquery', 'IlluminaHumanMethylation450kmanifest'
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.
Packages suggested but not available for checking: 'ClusterR', 'testthat'
Package unavailable to check Rd xrefs: 'ClusterR'
Packages suggested but not available for checking:
  'dbplyr', 'dplyr', 'testthat', 'tibble'
Running examples in 'mlr3db-Ex.R' failed
The error most likely occurred in:

> ### Name: DataBackendDplyr
> ### Title: DataBackend for dplyr/dbplyr
> ### Aliases: DataBackendDplyr
> 
> ### ** Examples
> 
> # Backend using a in-memory tibble
> data = tibble::as_tibble(iris)
Error in loadNamespace(x) : there is no package called 'tibble'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages suggested but not available for checking:
  'caret', 'FSelectorRcpp', 'testthat'
Packages unavailable to check Rd xrefs: 'caret', 'FSelectorRcpp'
Running examples in 'mlr3filters-Ex.R' failed
The error most likely occurred in:

> ### Name: mlr_filters_information_gain
> ### Title: Information Gain Filter
> ### Aliases: mlr_filters_information_gain FilterInformationGain
> 
> ### ** Examples
> 
> ## InfoGain (default)
> task = mlr3::tsk("pima")
> filter = flt("information_gain")
> filter$calculate(task)
Error: The following packages could not be loaded: FSelectorRcpp
Execution halted
Packages suggested but not available for checking:
  'farff', 'qs', 'testthat'
Packages suggested but not available for checking:
  'ggplot2', 'quanteda', 'testthat', 'bestNormalize', 'NMF'
Packages unavailable to check Rd xrefs: 'bestNormalize', 'NMF', 'quanteda'
Running examples in 'mlr3pipelines-Ex.R' failed
The error most likely occurred in:

> ### Name: mlr_pipeops_boxcox
> ### Title: Box-Cox Transformation of Numeric Features
> ### Aliases: mlr_pipeops_boxcox PipeOpBoxCox
> 
> ### ** Examples
> 
> library("mlr3")
> 
> task = tsk("iris")
> pop = po("boxcox")
> 
> task$data()
       Species Petal.Length Petal.Width Sepal.Length Sepal.Width
  1:    setosa          1.4         0.2          5.1         3.5
  2:    setosa          1.4         0.2          4.9         3.0
  3:    setosa          1.3         0.2          4.7         3.2
  4:    setosa          1.5         0.2          4.6         3.1
  5:    setosa          1.4         0.2          5.0         3.6
 ---                                                            
146: virginica          5.2         2.3          6.7         3.0
147: virginica          5.0         1.9          6.3         2.5
148: virginica          5.2         2.0          6.5         3.0
149: virginica          5.4         2.3          6.2         3.4
150: virginica          5.1         1.8          5.9         3.0
> pop$train(list(task))[[1]]$data()
Error: The following packages could not be loaded: bestNormalize
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("checkmate")
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'bujar', 'ggplot2', 'mlr3extralearners', 'testthat'
Package unavailable to check Rd xrefs: 'bujar'
Package required but not available: 'readxl'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mlr3viz'

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

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

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', 'randomForestSRC', 'FSelectorRcpp', 'lintr', 'Hmisc'

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

> ### Name: OptimizerInterMBO
> ### Title: Tuner and Optimizer using mlrMBO
> ### Aliases: OptimizerInterMBO mlr_optimizers_intermbo mlr_tuners_intermbo
> ###   TunerInterMBO
> 
> ### ** Examples
> 
> library("paradox")
> library("bbotk")
> 
> # silly example function: minimize x^2 for -1 < x < 1
> domain <- ParamSet$new(list(ParamDbl$new("x", lower = -1, upper = 1)))
> codomain <- ParamSet$new(list(ParamDbl$new("y", tags = "minimize")))
> objective <- ObjectiveRFun$new(function(xs) list(y = xs$x^2), domain, codomain)
> 
> # initialize instance
> instance <- OptimInstanceSingleCrit$new(objective, domain, trm("evals", n_evals = 6))
> 
> # use intermbo optimizer
> optser <- opt("intermbo")
> 
> # optimizer has hyperparameters from mlrMBO
> optser$param_set$values$final.method <- "best.predicted"
> 
> # optimization happens here.
> optser$optimize(instance)
INFO  [00:19:18.895] [bbotk] Starting to optimize 1 parameter(s) with '<OptimizerInterMBO>' and '<TerminatorEvals> [n_evals=6]' 
INFO  [00:19:19.799] [bbotk] Evaluating 4 configuration(s) 
INFO  [00:19:19.829] [bbotk] Result of batch 1: 
INFO  [00:19:19.835] [bbotk]           x          y 
INFO  [00:19:19.835] [bbotk]   0.7410401 0.54914037 
INFO  [00:19:19.835] [bbotk]  -0.2002171 0.04008688 
INFO  [00:19:19.835] [bbotk]   0.2467707 0.06089576 
INFO  [00:19:19.835] [bbotk]  -0.9068912 0.82245165 
Error in encall(self$r.session, vals, n.objectives, still.needs.proposition,  : 
  callr subprocess failed: there is no package called 'mlrMBO'
Calls: <Anonymous> ... <Anonymous> -> .__OptimizerInterMBO__.optimize -> encall
Execution halted
Running 'run.R'
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', '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', 'caret', 'ClusterR', 'cowplot', 'fda.usc', 'forecast',
  'FSelectorRcpp', 'ggpubr', 'Hmisc', 'klaR', 'lintr', 'mlrMBO', 'pec',
  'randomForestSRC', 'refund', 'rrlda', 'sf', 'smoof', 'testthat',
  'tidyr', 'tsfeatures', 'vdiffr'

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

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

Packages suggested but not available for checking:
  'bshazard', 'MIICD', 'dynsurv', 'AER', 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  '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', 'tidygraph', 'ggraph', 'ggforce'
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 76-80 (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
Error(s) in re-building vignettes:
--- re-building 'MM2Sdata.Rnw' using knitr
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "MM2Sdata.tex" ' had status 1
Error: processing vignette 'MM2Sdata.Rnw' failed with diagnostics:
running 'texi2dvi' on 'MM2Sdata.tex' failed

LaTeX errors:
.Rcheck/vign_test/MM2Sdata/vignettes/MM2Sdata.tex:153: pdfTeX error (font expan
sion): auto expansion is only possible with scalable fonts.
<argument> ...shipout:D \box_use:N \l_shipout_box 
                                                  \__shipout_drop_firstpage_...
l.153 ... 'citation("{}pkgname"{})'.}}\end{kframe}
.Rcheck/vign_test/MM2Sdata/vignettes/MM2Sdata.tex:153:  ==> Fatal error occurre
d, no output PDF file produced!

--- failed re-building 'MM2Sdata.Rnw'

SUMMARY: processing the following file failed:
  'MM2Sdata.Rnw'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'testthat', 'caret', 'ggplot2', 'ggpubr', 'cowplot',
  'philentropy'
Namespaces in Imports field not imported from:
  'datasets' 'doParallel' 'parallel'
  All declared Imports should be used.
Running 'helpers.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Cluster-Analysis.rmd' using rmarkdown
Quitting from lines 26-95 (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
Packages required but not available: 'adegenet', 'pegas'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'aMNLFA', 'GPCMlasso'
Error(s) in re-building vignettes:
--- re-building 'OVA_Predictions_For_MNL.Rmd' using rmarkdown
Quitting from lines 78-89 (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
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'tibble'

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

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'sads'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'highcharter', 'leaflet', 'plotly', 'sunburstR', 'treemap'

Package suggested but not available for checking: 'modgetxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'modcmfitrOverview.Rmd' using rmarkdown
Quitting from lines 304-389 (modcmfitrOverview.Rmd) 
Error: processing vignette 'modcmfitrOverview.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'modcmfitrOverview.Rmd'

SUMMARY: processing the following file failed:
  'modcmfitrOverview.Rmd'

Error: Vignette re-building failed.
Execution halted
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', 'dplyr', 'gganimate', 'ggplot2', 'merTools', 'rstanarm',
  'see', 'testthat'
Packages required but not available: 'dplyr', 'plotly'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rms', 'randomForestSRC'
Running examples in 'ModelGood-Ex.R' failed
The error most likely occurred in:

> ### Name: AutoSelectLRM
> ### Title: Automated backward elemination for logistic regression
> ### Aliases: AutoSelectLRM
> 
> ### ** Examples
> 
> library(rms)
Error in library(rms) : there is no package called 'rms'
Execution halted
Packages required but not available: 'caret', 'dplyr', 'ggplot2'

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

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

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

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

Packages suggested but not available for checking: 'ggDCA', 'rms'

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

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', 'kableExtra', 'tidyr'

Packages suggested but not available for checking:
  'AER', 'broom.mixed', 'ggplot2', 'gt', 'IRdisplay', 'testthat',
  'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'modeltime', 'modeltime.resample', 'tune', 'rsample', 'yardstick',
  'workflows', 'parsnip', 'recipes', 'timetk', 'tibble', 'dplyr',
  'tidyr', 'cli'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'StanHeaders', 'timetk', 'parsnip', 'dials', 'yardstick',
  'workflows', 'hardhat', 'plotly', 'gt', 'ggplot2', 'tibble', 'tidyr',
  'dplyr', 'forcats', 'janitor', 'forecast', 'prophet', 'cli'

Packages suggested but not available for checking:
  'rstan', 'tidymodels', 'workflowsets', 'recipes', 'rsample', 'tune',
  'tidyverse', 'testthat', 'roxygen2', 'thief', 'tidyquant'

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',
  'forcats', 'ggplot2', 'plotly', 'cli'

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

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

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

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 unavailable to check Rd xrefs: 'roxygen2'
Package required but not available: 'sf'

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

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

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'httptest', 'leafem', 'leaflet', 'mapedit',
  'shinyFiles', 'testthat', 'tibble', 'tidyr'

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

> ### Name: marg.ivreg
> ### Title: Predicted Margins for 'ivreg' objects from the 'AER' package
> ### Aliases: marg.ivreg
> 
> ### ** Examples
> 
> # From ?AER::ivreg
> 
> # data
> data("CigarettesSW", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: data -> find.package
Execution halted
Packages suggested but not available for checking: 'BioStatR', 'ggplot2'
Running examples in 'ModStatR-Ex.R' failed
The error most likely occurred in:

> ### Name: boot.mcor.ic
> ### Title: Intervalles de confiance bootstrap pour une matrice de
> ###   corr<c3><a9>lation 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: 'car', 'NeuralNetTools', 'AER'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', 'lintr'
Packages suggested but not available for checking:
  'smoof', 'testthat', 'ggplot2', 'pkgdown'
Error(s) in re-building vignettes:
--- re-building 'Basic_Usage.Rmd' using rmarkdown
Quitting from lines 106-114 (Basic_Usage.Rmd) 
Error: processing vignette 'Basic_Usage.Rmd' failed with diagnostics:
there is no package called 'smoof'
--- failed re-building 'Basic_Usage.Rmd'

--- re-building 'Comparison_Usage.Rmd' using rmarkdown
Quitting from lines 243-278 (Comparison_Usage.Rmd) 
Error: processing vignette 'Comparison_Usage.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Comparison_Usage.Rmd'

--- re-building 'Modification_Usage.Rmd' using rmarkdown
Quitting from lines 70-94 (Modification_Usage.Rmd) 
Error: processing vignette 'Modification_Usage.Rmd' failed with diagnostics:
there is no package called 'smoof'
--- failed re-building 'Modification_Usage.Rmd'

--- re-building 'problem-definition.Rmd' using rmarkdown
--- finished re-building 'problem-definition.Rmd'

--- re-building 'writing-functions-for-moeadr.Rmd' using rmarkdown
--- finished re-building 'writing-functions-for-moeadr.Rmd'

SUMMARY: processing the following files failed:
  'Basic_Usage.Rmd' 'Comparison_Usage.Rmd' 'Modification_Usage.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'clustMD'
Package unavailable to check Rd xrefs: 'clustMD'
Packages required but not available: 'tibble', 'readr', 'cli', '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: 'tidyr', 'compareDF'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'mockery', 'tibble'
Packages required but not available: 'ggplot2', 'ggridges'

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: 'testthat', 'patrick'
Package required but not available: 'crawl'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'nycflights13', 'ggplot2'
Packages required but not available: 'dplyr', 'Hmisc'

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

Packages suggested but not available for checking: '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.
Package required but not available: 'taxize'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'MonteCarlo-Vignette.Rmd' using rmarkdown
Quitting from lines 316-320 (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:
  'dplyr', 'ggplot2', 'tidytext', 'ggwordcloud', 'RMariaDB', 'cli'

Package suggested but not available for checking: 'testthat'

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

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', 'tibble', 'readr'
Packages required but not available: 'iml', 'pdp', 'vip', 'ggplot2'

Packages suggested but not available for checking:
  'GDAtools', 'caret', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'testthat', 'roxygen2'
Package required but not available: 'oce'

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', 'tidyr', 'dplyr', 'ggplot2'

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

Package suggested but not available for checking: 'tidyverse'

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

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

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'

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

> ### Name: HeatX
> ### Title: Data from a heat exchanger laboratory
> ### Aliases: HeatX
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # We can test for heat exchange with the environment by checking to see if the 
> # heat gained by the cold water matches the heat lost by the hot water.
> C_p <- 4.182 / 60  # / 60 because measuring m in L/min
> HeatX2 <- 
+   dplyr::mutate(HeatX,
+     Q.cold = m.cold * C_p * (T.cold.out - T.cold.in),
+     Q.hot  = m.hot * C_p * (T.hot.out- T.hot.in),
+     Q.env  = Q.cold + Q.hot
+   )
Error in loadNamespace(x) : there is no package called 'dplyr'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'mosaic-vignette.Rmd' using rmarkdown
Quitting from lines 55-192 (mosaic-vignette.Rmd) 
Error: processing vignette 'mosaic-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'mosaic-vignette.Rmd'

SUMMARY: processing the following file failed:
  'mosaic-vignette.Rmd'

Error: Vignette re-building failed.
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', 'ggformula', 'mosaicCore', 'ggplot2', 'ggstance',
  'ggridges', 'ggrepel', 'tidyr', 'readr', 'ggdendro', 'broom',
  'leaflet'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ecr', 'smoof', 'mlrCPO', 'mlr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'NlcOptim'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'bigstatsr', 'scatterpie', 'ggplot2', 'ggpmisc', 'ggthemes',
  'testthat', 'viridis'
Error(s) in re-building vignettes:
--- re-building 'MOSS_working_example.Rmd' using rmarkdown
Quitting from lines 134-144 (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
Packages required but not available: 'MBESS', 'ez'

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

Package suggested but not available for checking: 'testthat'

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

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

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

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

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

Package suggested but not available for checking: 'testthat'

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

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 suggested but not available for checking:
  'ggmap', 'testthat', 'ggplot2', 'leaflet', 'amt'
Package unavailable to check Rd xrefs: 'amt'
Error(s) in re-building vignettes:
--- re-building 'browseMovebank.Rmd' using rmarkdown
--- finished re-building 'browseMovebank.Rmd'

--- re-building 'move.Rmd' using rmarkdown
Loading required package: geosphere
Loading required package: sp
Loading required package: raster
Loading required package: rgdal
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
Path to GDAL shared files: C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/rgdal/gdal
GDAL binary built with GEOS: FALSE 
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/rgdal/proj

Attaching package: 'lubridate'

The following objects are masked from 'package:raster':

    intersect, union

The following objects are masked from 'package:base':

    date, intersect, setdiff, union

Quitting from lines 334-338 (move.Rmd) 
Error: processing vignette 'move.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'move.Rmd'

SUMMARY: processing the following file failed:
  'move.Rmd'

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

Packages suggested but not available for checking:
  'mapview', 'leaflet', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library('testthat')
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'ggpubr', 'tibble', 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'markovchain', 'matlib'
Running examples in 'MPkn-Ex.R' failed
The error most likely occurred in:

> ### Name: MPkn-package
> ### Title: Calculations of One Discrete Model in Several Time Steps
> ### Aliases: MPkn-package
> 
> ### ** Examples
> 
> require(MPkn)
> require(markovchain)
Loading required package: markovchain
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'markovchain'
> options(digits = 14)
> n = 12
> k = 2
> rz = 11
> P = array(0, c(rz, rz))
> for (i in 1:rz){
+   po = runif(rz)
+   P[i, ] = po/sum(po)
+ }
> I = diag(1, rz, rz)
> Myy = MUPkL(P, P, I, n, k, c(1:rz))
> StSy = NULL
> for (i in 1:rz) StSy = c(StSy, Myy$Navg[,,i][n])
> mrkv = new("markovchain", transitionMatrix = P)
Error in getClass(Class, where = topenv(parent.frame())) : 
  "markovchain" is not a defined class
Calls: new -> getClass
Execution halted
Packages required but not available: 'ggplot2', 'fastDummies'

Packages suggested but not available for checking: 'rhdf5', 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'devtools'

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

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

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

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

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

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

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

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:
  'GGally', 'Hmisc', 'mice', 'network', 'sna', 'WGCNA'

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 unavailable to check Rd xrefs: 'rstan'
Packages required but not available: 'ggplot2', 'ggfortify', 'plotly'

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

Packages suggested but not available for checking: 'GA', 'hydroPSO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'mscstexta4r'
Running 'testthat.R'
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
Packages required but not available: 'dplyr', 'ggplot2'

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

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.
Packages suggested but not available for checking: 'ggplot2', 'sna'
Running examples in 'MSG-Ex.R' failed
The error most likely occurred in:

> ### 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
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'ggbeeswarm', 'tidyr'

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'

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'

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

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.
Packages suggested but not available for checking:
  'mstate', 'testthat', 'flexsurv'
Packages unavailable to check Rd xrefs: 'flexsurv', 'mstate'
Running 'test_base.R'
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
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: 'testthat'

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

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

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

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

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'Rsctest.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'sf', 'cartography'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'mthapower-Ex.R' failed
The error most likely occurred in:

> ### Name: mthapower
> ### Title: Power calculations - mtDNA haplogroups
> ### Aliases: mthapower
> 
> ### ** Examples
> 
> # Example 1:
> pow <- mthapower(n.cases=203, p0=0.443, Nh=13, OR.cas.ctrl=2.33, sig.level=0.05)
> 
> # Example 2:
> # Create data frames
> pow.H150 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.5, sig.level=0.05)
> pow.H175 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.75, sig.level=0.05)
> pow.H200 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2, sig.level=0.05)
> pow.H250 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2.5, sig.level=0.05)
> 
> # Bind the three data frames:
> bindata <- rbind(pow.H150,pow.H175,pow.H200,pow.H250)
> # Adds column OR to binded data frame:
> bindata$OR <- rep(factor(c(1.50,1.75,2,2.5)),
+               times = c(nrow(pow.H150),
+                         nrow(pow.H175),
+                         nrow(pow.H200),
+                         nrow(pow.H250)))
> # Create plot:
> # install.packages("car")
> library(car)
Error in library(car) : there is no package called 'car'
Execution halted
Running examples in 'MTLR-Ex.R' failed
The error most likely occurred in:

> ### 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
Error(s) in re-building vignettes:
--- re-building 'workflow.Rmd' using rmarkdown
Quitting from lines 136-137 (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
Error(s) in re-building vignettes:
--- re-building 'Guide.Rmd' using rmarkdown
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-2
Loading required package: rpart
Loading required package: MASS
Loading required package: e1071
Loading required package: class
Quitting from lines 174-188 (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
Package required but not available: 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Matrix' 'capushe' 'shiny'
  All declared Imports should be used.
Packages required but not available:
  'ggplot2', 'dplyr', 'tibble', 'readr', 'tidyr'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'shape'
  All declared Imports should be used.
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: 'pgirmess'
Package required but not available: 'RcppParallel'

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: 'nbpMatching', 'crossmatch'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'multiFit.Rmd' using rmarkdown
Quitting from lines 79-83 (multiFit.Rmd) 
Error: processing vignette 'multiFit.Rmd' failed with diagnostics:
there is no package called 'qgraph'
--- failed re-building 'multiFit.Rmd'

SUMMARY: processing the following file failed:
  'multiFit.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'statnet', 'testthat'
Packages required but not available:
  'RcppParallel', 'rstan', 'rstantools', 'tibble', 'dplyr', 'forcats',
  'tidyr', 'ggraph', 'ggplot2', 'ggdist', 'bayesplot', 'StanHeaders'

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

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

Package suggested but not available for checking: 'roxygen2'

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

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

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

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:
  'ggplot2', 'testthat', 'broom', 'gganimate', 'forcats', 'cowplot',
  'tidybayes', 'modelr', 'styler'

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

Depends: includes the non-default packages:
  'car', 'pdist', 'pls', 'gplots', 'mvtnorm', 'robustbase', 'gtools',
  'bitops', 'caTools', 'pcaPP', 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Packages which this enhances but not available for checking:
  'cplm', 'logistf', 'spdep', 'spatialreg', 'splm'
Packages unavailable to check Rd xrefs: 'arm', 'geepack', 'wgeesel', 'cplm', 'spatialreg', 'splm', 'logistf'
Running examples in 'munsell-Ex.R' failed
The error most likely occurred in:

> ### 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 examples in 'musica-Ex.R' failed
The error most likely occurred in:

> ### Name: compare
> ### Title: Compare decomposed variables
> ### Aliases: compare
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'using_musica.Rmd' using rmarkdown
Quitting from lines 17-20 (using_musica.Rmd) 
Error: processing vignette 'using_musica.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'using_musica.Rmd'

SUMMARY: processing the following file failed:
  'using_musica.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'plsgenomics'
Packages required but not available: 'qs', '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: 'qvalue', 'testthat'
Running examples in 'mutoss-Ex.R' failed
The error most likely occurred in:

> ### 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
Package required but not available: 'ggplot2'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package unavailable to check Rd xrefs: 'sampleSelection'
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tidytext'
Error(s) in re-building vignettes:
--- re-building 'getting_started_with_mvrsquared.Rmd' using rmarkdown
Quitting from lines 150-183 (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', 'rdryad'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'mwaved-Ex.R' failed
The error most likely occurred in:

> ### Name: multiWaveD
> ### Title: Full mWaveD analysis
> ### Aliases: multiWaveD
> 
> ### ** Examples
> 
> library(mwaved)
> # Simulate the multichannel doppler signal.
> m <- 3
> n <- 2^10
> signal <- makeDoppler(n)
> # Noise levels per channel
> e <- rnorm(m * n)
> # Create Gamma blur
> shape <- seq(from = 0.5, to = 1, length = m)
> scale <- rep(0.25, m)
> G <- gammaBlur(n, shape = shape, scale = scale)
> # Convolve the signal
> X <- blurSignal(signal, G)
> # Create error with custom signal to noise ratio
> SNR <- c(10, 15, 20)
> sigma <- sigmaSNR(X, SNR)
> if (requireNamespace("fracdiff", quietly = TRUE)) {
+   alpha <- c(0.75, 0.8, 1)
+ } else {
+   alpha <- rep(1, m)
+ }
> E <- multiNoise(n, sigma, alpha)
> # Create noisy & blurred multichannel signal
> Y <- X + E
> # Compute mWaveD object
> mWaveDObj <- multiWaveD(Y, G = G, alpha = alpha)
> plot(mWaveDObj)
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'mWaveD.Rmd' using rmarkdown
Quitting from lines 14-53 (mWaveD.Rmd) 
Error: processing vignette 'mWaveD.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'mWaveD.Rmd'

SUMMARY: processing the following file failed:
  'mWaveD.Rmd'

Error: Vignette re-building failed.
Execution halted
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 (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
Package required but not available: 'OpenMx'

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: 'geepack', 'dplyr', 'Hmisc'

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

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: 'rms', 'mclogit'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
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'
Packages required but not available:
  'cli', 'dplyr', 'ggbeeswarm', 'ggforce', 'ggplot2', 'ggrepel',
  'sessioninfo', 'tibble', 'tidyr'

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

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

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.
Packages suggested but not available for checking:
  'readxl', 'testthat', 'usethis'
Packages suggested but not available for checking:
  'testthat', 're2r', 'dplyr', 'tidyr', 'rematch2'
Error(s) in re-building vignettes:
--- re-building 'v1-old-syntax.Rmd' using knitr
--- finished re-building 'v1-old-syntax.Rmd'

--- re-building 'v2-recommended-syntax.Rmd' using knitr
--- finished re-building 'v2-recommended-syntax.Rmd'

--- re-building 'v3-verbose.Rmd' using knitr
Quitting from lines 40-107 (v3-verbose.Rmd) 
Error: processing vignette 'v3-verbose.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'v3-verbose.Rmd'

--- re-building 'v4-data-frames.Rmd' using knitr
Quitting from lines 40-146 (v4-data-frames.Rmd) 
Error: processing vignette 'v4-data-frames.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'v4-data-frames.Rmd'

SUMMARY: processing the following files failed:
  'v3-verbose.Rmd' 'v4-data-frames.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'autothresholdr', 'detrendr', 'dplyr', 'ggplot2', 'ijtiff', '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', 'tidyr', 'tibble', 'visdat', 'forcats',
  'viridis', 'UpSetR'

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

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:
  'ggplot2', 'rnaturalearth', 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'spatialClust', 'ggplot2'
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.
Running 'spelling.R'
  Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'caret', 'ggplot2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'issue-1.R'
Running the tests in 'tests/issue-1.R' failed.
Complete output:
  > stopifnot(require(testthat))
  Loading required package: testthat
  Error: require(testthat) is not TRUE
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  Execution halted
Namespace in Imports field not imported from: 'tuneR'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'tidyr'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Deriv' 'compiler' 'stringi'
  All declared Imports should be used.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'cowplot', 'dplyr', 'ggplotify', 'plotly', 'ggrepel', 'shadowtext',
  'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 're2r', 'ggplot2', 'tidyr'
Packages required but not available: 'network', 'networkDynamic', 'sna'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'run_tests.R'
Running the tests in 'tests/run_tests.R' failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'RDS', 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'neonUtilities', 'rhdf5'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'tibble', 'testthat', 'neonUtilities', 'rhdf5'

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: 'rhdf5', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Matrix' 'igraph'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'tibble', 'ggfortify', 'ggplot2', 'ggraph'

Package suggested but not available for checking: 'testthat'

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

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', 'msigdbr', 'ndexr', 'RCy3'

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

Packages suggested but not available for checking:
  'fastshp', 'sf', 'SpaDES.core', 'testthat'

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

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: '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', 'sna', 'qgraph', 'network', 'ggrepel', 'GGally',
  'ggvis'

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

Package suggested but not available for checking: 'networktools'

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:
  'broom', 'dplyr', 'ggplot2', 'network', 'sna', 'tidyr'

Package suggested but not available for checking: 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'mgcv' 'stats'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'ggrepel'

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: 'tibble'

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

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

Package suggested but not available for checking: 'testthat'

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

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

Package suggested but not available for checking: 'fxregime'

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: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'NeuralNetTools', 'caret', 'fastDummies', 'Hmisc',
  'ggforce', 'ggnewscale'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'neurobase-Ex.R' failed
The error most likely occurred in:

> ### 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
Error(s) in re-building vignettes:
--- re-building 'neurobase.Rmd' using rmarkdown
--- finished re-building 'neurobase.Rmd'

--- re-building 'nifti_basics.Rmd' using rmarkdown
Quitting from lines 11-19 (nifti_basics.Rmd) 
Error: processing vignette 'nifti_basics.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'nifti_basics.Rmd'

--- re-building 'simple_io.Rmd' using rmarkdown
trying URL 'https://johnmuschelli.com/open_ms_data/cross_sectional/raw/patient01/T1W.nii.gz'
 length 21807043 bytes (20.8 MB)
==================================================
downloaded 20.8 MB

--- finished re-building 'simple_io.Rmd'

SUMMARY: processing the following file failed:
  'nifti_basics.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'hcp.Rmd' using rmarkdown
Quitting from lines 15-18 (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:
  '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: 'devtools', 'tidyr'

Packages suggested but not available for checking:
  'dplyr', 'rvest', '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.
Packages required but not available: 'quanteda', 'quanteda.textstats'

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: 'lintr', 'testthat'
Running examples in 'nFCA-Ex.R' failed
The error most likely occurred in:

> ### Name: nfca
> ### Title: Numerical Formal Concept Analysis for Systematic Clustering
> ### Aliases: nfca
> 
> ### ** Examples
> 
> # View a build-in correlation matrix: nfca_example
> data("nfca_example", package = "nFCA")
> nfca_example
      H    W    S    D   HF   HM   WF   WM   H1   W1    O
1  1.00 0.95 0.90 0.90 0.85 0.85 0.80 0.80 0.40 0.30 0.10
2  0.95 1.00 0.88 0.88 0.70 0.70 0.87 0.87 0.20 0.45 0.15
3  0.90 0.88 1.00 0.82 0.80 0.80 0.76 0.76 0.10 0.10 0.02
4  0.90 0.88 0.82 1.00 0.82 0.82 0.81 0.81 0.10 0.10 0.05
5  0.85 0.70 0.80 0.82 1.00 0.95 0.65 0.65 0.08 0.06 0.01
6  0.85 0.70 0.80 0.82 0.95 1.00 0.60 0.60 0.06 0.07 0.01
7  0.80 0.87 0.76 0.81 0.65 0.60 1.00 0.95 0.03 0.05 0.01
8  0.80 0.87 0.76 0.81 0.65 0.60 0.95 1.00 0.01 0.02 0.01
9  0.40 0.20 0.10 0.10 0.08 0.06 0.03 0.01 1.00 0.02 0.01
10 0.30 0.45 0.10 0.10 0.06 0.07 0.05 0.02 0.02 1.00 0.02
11 0.10 0.15 0.02 0.05 0.01 0.01 0.01 0.01 0.01 0.02 1.00
>      
> # 1. using the default 'histogram' method and choosing threshold
> # automatically   
> nfca(data = nfca_example)
Warning in system("ruby multistagefca.rb") : 'ruby' not found
Warning in file.rename("example.dot", "example.txt") :
  cannot rename file 'example.dot' to 'example.txt', reason 'The system cannot find the file specified'
Warning in file(file, "rt") :
  cannot open file 'example.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: nfca ... thresholdTEST -> as.matrix -> read.csv -> read.table -> file
Execution halted
Packages required but not available:
  'dplyr', 'janitor', 'nflfastR', 'tibble', 'tidyr'

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'lamW'
Packages required but not available:
  'dplyr', 'cli', '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: 'fields', 'car'

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

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

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

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

Packages suggested but not available for checking:
  'wikilake', 'testthat', 'lwgeom'

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

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', 'caret', 'readr', 'rsample', 'ggplot2', 'ggrepel', 'tidyr',
  'forcats', 'janitor', 'synthpop'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'rgdal' 'sp'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'ggthemes', 'dplyr'

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

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

Package suggested but not available for checking: 'testthat'

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

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

Package suggested but not available for checking: 'ggplot2'

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.
Namespace in Imports field not imported from: 'rjson'
  All declared Imports should be used.
Packages suggested but not available for checking: 'dplyr', 'skimr', 'sf'
Packages suggested but not available for checking:
  'testthat', 'sf', 'leaflet'
Packages unavailable to check Rd xrefs: 'leaflet', 'sf'
Running examples in 'nlgeocoder-Ex.R' failed
The error most likely occurred in:

> ### Name: nl_geocode
> ### Title: Geocode adresses
> ### Aliases: nl_geocode nl_geocode_rd nl_geocode_df
> 
> ### ** Examples
> 
> data("addresses")
> 
> r <- nl_geocode(addresses$Address)
Error in nl_geocode(addresses$Address) : You'll need package 'sf'.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'geocode.Rmd' using rmarkdown
Quitting from lines 15-22 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building 'geocode.Rmd'

SUMMARY: processing the following file failed:
  'geocode.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'Pwr1.R'
Running the tests in 'tests/Pwr1.R' failed.
Complete output:
  > date()
  [1] "Thu Aug  5 00:44:08 2021"
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'RxODE', 'StanHeaders'

Packages suggested but not available for checking:
  'broom.mixed', 'devtools', 'dotwhisker', 'dplyr', 'ggtext',
  'patchwork', 'pkgdown', 'testthat', 'tidyr', 'vpc', 'xgxr', 'xpose',
  'tibble', 'cli', 'qs', 'forecast'

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.
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 (Bootstrapping.Rmd) 
Error: processing vignette 'Bootstrapping.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Bootstrapping.Rmd'

--- re-building 'Models-and-Functions.Rmd' using rmarkdown
Quitting from lines 15-20 (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 (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-Oddi-LFMC.Rmd' using rmarkdown
Quitting from lines 15-22 (nlraa-Oddi-LFMC.Rmd) 
Error: processing vignette 'nlraa-Oddi-LFMC.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'nlraa-Oddi-LFMC.Rmd'

--- re-building 'nlraa.Rmd' using rmarkdown
Quitting from lines 15-18 (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' 'Models-and-Functions.Rmd'
  'nlraa-AgronJ-paper.Rmd' 'nlraa-Oddi-LFMC.Rmd' 'nlraa.Rmd'

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

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:
  'ggplot2', 'broom', 'testthat'

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

    %*%, diag, diag<-, lower.tri, upper.tri

! Undefined control sequence.
<argument> {\proglang 
                      {R}}: A Language and Environment for Statistical Compu...
l.5074 Environment for Statistical Computing}
                                             . Vienna, Austria: R Foundation 

! pdflatex: major issue: User/administrator updates are out-of-sync.

Error: processing vignette 'nlsr-derivs.Rmd' failed with diagnostics:
LaTeX failed to compile C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/nlsr/nlsr.Rcheck/vign_test/nlsr/vignettes/nlsr-derivs.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See nlsr-derivs.log for more info.
--- failed re-building 'nlsr-derivs.Rmd'

--- re-building 'nlsr-devdoc.Rmd' using rmarkdown
--- finished re-building 'nlsr-devdoc.Rmd'

SUMMARY: processing the following file failed:
  'nlsr-derivs.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'Hmisc', 'testthat'
Namespace in Imports field not imported from: 'deSolve'
  All declared Imports should be used.
Running examples in 'nLTT-Ex.R' failed
The error most likely occurred in:

> ### Name: get_branching_times
> ### Title: Collect the branching times from the stem age
> ### Aliases: get_branching_times
> 
> ### ** Examples
> 
>   phylogeny <- ape::read.tree(text = "((a:2,b:2):1,c:3);")
>   phylogeny$root.edge <- 2 # nolint ape variable name
>   testthat::expect_true(
+     all(nLTT::get_branching_times(phylogeny) == c(5, 3, 2)))
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 'get_nltt_values.Rmd' using rmarkdown
Quitting from lines 65-70 (get_nltt_values.Rmd) 
Error: processing vignette 'get_nltt_values.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'get_nltt_values.Rmd'

--- re-building 'nltt_diff.Rmd' using rmarkdown
Quitting from lines 91-95 (nltt_diff.Rmd) 
Error: processing vignette 'nltt_diff.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building 'nltt_diff.Rmd'

--- re-building 'nltts_plot.Rmd' using rmarkdown
--- finished re-building 'nltts_plot.Rmd'

--- re-building 'stretch_nltt_matrix.Rmd' using rmarkdown
--- finished re-building 'stretch_nltt_matrix.Rmd'

--- re-building 'trees_with_root_edge.Rmd' using rmarkdown
--- finished re-building 'trees_with_root_edge.Rmd'

--- re-building 'walkthrough.Rmd' using rmarkdown
--- finished re-building 'walkthrough.Rmd'

SUMMARY: processing the following files failed:
  'get_nltt_values.Rmd' 'nltt_diff.Rmd'

Error: Vignette re-building failed.
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: 'netmeta', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'DataCreate.Rmd' using rmarkdown
Quitting from lines 29-36 (DataCreate.Rmd) 
Error: processing vignette 'DataCreate.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'DataCreate.Rmd'

--- re-building 'NMdata-FAQ.Rmd' using rmarkdown
--- finished re-building 'NMdata-FAQ.Rmd'

--- re-building 'NMscanData.Rmd' using rmarkdown
Quitting from lines 107-112 (NMscanData.Rmd) 
Error: processing vignette 'NMscanData.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'NMscanData.Rmd'

SUMMARY: processing the following files failed:
  'DataCreate.Rmd' 'NMscanData.Rmd'

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

Package suggested but not available for checking: 'recipes'

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

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.
Packages required but not available: 'sf', 'lwgeom'

Package suggested but not available for checking: 'stars'

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

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

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'ggridges', 'tidyr', 'forcats', 'mlr', 'mlrCPO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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',
  'tibble', 'tidyr', 'viridis'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'dbplyr', 'readr', 'testthat', 'tibble', 'vroom'
Running examples in 'noctua-Ex.R' failed
The error most likely occurred in:

> ### 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
Packages required but not available:
  'tibble', 'dplyr', 'ggplot2', 'Rsamtools', 'philentropy'

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: 'testthat', 'waldo'
Packages required but not available: 'tibble', 'readr', 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'shinytest'
Packages required but not available: 'rms', 'do', 'Hmisc'

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

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

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

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:
  'AER', 'mlogit', 'testthat'
Packages required but not available: 'Hmisc', 'rms'

Depends: includes the non-default packages:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Package suggested but not available for checking: 'ggfortify'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'tidyverse', 'ggplot2', 'ggnetwork', 'intergraph',
  'viridis', 'gganimate', 'tidytree', 'treeio', 'ggtree', 'dplyr'
Packages unavailable to check Rd xrefs: 'tidytree', 'treeio'
Packages suggested but not available for checking: 'brms', 'testthat'
Running examples in 'novelforestSG-Ex.R' failed
The error most likely occurred in:

> ### Name: download_model
> ### Title: Download Model Fitted to the 'novelforest' Data
> ### Aliases: download_model
> 
> ### ** Examples
> 
> novelforest_model <- download_model()
To save the model locally, use argument save_to = 'path/filename.rds'
Downloading model (size: 16.5 Mb)
> 
> # library(brms)  # recommended
> summary(novelforest_model)
Loading required package: rstan
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rstan'
Error in .requirePackage(package) : 
  unable to find required package 'rstan'
Calls: summary ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'bayesplot'

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

Package suggested but not available for checking: 'car'

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

Package suggested but not available for checking: 'styler'

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: 'dplyr', 'FDRreg', 'Hmisc', 'mosaic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'rts'
  All declared Imports should be used.
Package required but not available: 'readxl'

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

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

--- re-building 'example1.Rmd' using rmarkdown
Quitting from lines 22-25 (example1.Rmd) 
Error: processing vignette 'example1.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'example1.Rmd'

--- re-building 'example2.Rmd' using rmarkdown
Quitting from lines 22-25 (example2.Rmd) 
Error: processing vignette 'example2.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'example2.Rmd'

SUMMARY: processing the following files failed:
  'example1.Rmd' 'example2.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'CCA', 'roxygen2', 'testthat'
Package required but not available: 'rvest'

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: 'readr', 'rvest', '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: 'mlr', 'rPref'

Package suggested but not available for checking: 'testthat'

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

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

> ### Name: nsrr_all_dataset_files
> ### Title: NSRR All Dataset files
> ### Aliases: nsrr_all_dataset_files
> 
> ### ** Examples
> 
> dataset = "shhs"
> df = nsrr_all_dataset_files(dataset, max_files = 10)
[1] "biostatistics-with-r"
[1] "datasets"
> testthat::expect_lte(nrow(df), 20)
Error in loadNamespace(x) : there is no package called 'testthat'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'iCAMP'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MASS' 'Rdpack' 'base' 'graphics' 'parallel'
  All declared Imports should be used.
Packages required but not available:
  'tsibble', 'forecast', 'ggplot2', 'dplyr', 'tidyr', 'tibble',
  'viridis'

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

> ### 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
Error(s) in re-building vignettes:
--- re-building 'README.Rmd' using rmarkdown
Quitting from lines 47-59 (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
Packages required but not available: 'ggplot2', 'outbreaker2'

Packages suggested but not available for checking:
  'testthat', 'tigris', 'sf', 'socialmixr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Errors in running code in vignettes:
when running code in 'oaih.Rnw'

> library("OAIHarvester")

> baseurl <- "http://epub.wu.ac.at/cgi/oai2"

> if (inherits(tryCatch(oaih_identify(baseurl), error = identity), 
+     "error")) q()
> proc.time()
   user  system elapsed 
   0.43    0.10   10.53 

... incomplete output.  Crash?

  'oaih.Rnw' using 'UTF-8'... failed to complete the test
Package required but not available: 'spdep'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available:
  'pec', 'dplyr', 'ggthemes', 'tidyr', 'ggplot2'

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

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: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bib2df', 'BIEN', 'dplyr', 'rgbif', 'taxize', 'leaflet', 'ggplot2',
  'tidyr', 'viridis', 'waffle'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'leaflet', 'leaflet.extras', 'ggplot2', 'dplyr', 'lwgeom',
  'mapview'

Package suggested but not available for checking: 'rio'

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

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

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

Packages suggested but not available for checking: 'marmap', 'ocedata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'DBItest', 'testthat', 'tibble'
Packages required but not available:
  'caret', 'ggplot2', 'tibble', 'ggthemes'

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 suggested but not available for checking:
  'mockery', 'pkgbuild', 'pkgload', 'testthat'
Package unavailable to check Rd xrefs: 'pkgbuild'
Packages suggested but not available for checking: 'sf', 'lwgeom'
Running examples in 'od-Ex.R' failed
The error most likely occurred in:

> ### Name: coords_to_od
> ### Title: Convert coordinates into a data frame of origins and
> ###   destinations
> ### Aliases: coords_to_od
> 
> ### ** Examples
> 
> p = sf::st_coordinates(od_data_centroids[1:3, ])
Error in loadNamespace(x) : there is no package called 'sf'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'tinytest.R'
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("od")
  + }
  
  test_od.R.....................    0 tests    
  test_od.R.....................    0 tests    
  test_od.R.....................    1 tests [0;32mOK[0m 
  test_od.R.....................    1 tests [0;32mOK[0m 
  test_od.R.....................    1 tests [0;32mOK[0m 0 origins with no match in zone ids
  0 destinations with no match in zone ids
  Error in od_coordinates(x, z, zd, silent = silent) : 
    sf package required, to install it see https://github.com/r-spatial/sf#installing
  Calls: <Anonymous> ... isTRUE -> is -> od_to_sf -> od_to_sfc -> od_coordinates
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'od.Rmd' using rmarkdown
Quitting from lines 134-144 (od.Rmd) 
Error: processing vignette 'od.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building 'od.Rmd'

SUMMARY: processing the following file failed:
  'od.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'oecd_vignette_main.Rmd' using knitr
Quitting from lines 122-130 (oecd_vignette_main.Rmd) 
Error: processing vignette 'oecd_vignette_main.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'oecd_vignette_main.Rmd'

SUMMARY: processing the following file failed:
  'oecd_vignette_main.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
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
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: 'dplyr', '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: 'car', 'ggplot2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'UpSetR'
Package unavailable to check Rd xrefs: 'UpSetR'
Error(s) in re-building vignettes:
--- re-building 'OmicNavigatorAPI.Rnw' using Sweave
OmicNavigator R package version: 1.4.2
The app is not installed. Install it with installApp()
Installing study "ABC" in C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/OmicNavigator/tmp/RtmpIVyUfO/file37442c9a28c0
Exporting study "ABC" as an R package
Calculating pairwise overlaps. This may take a while...
Exported study to C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\OmicNavigator\tmp\RtmpIVyUfO/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 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/OmicNavigator/tmp/RtmpIVyUfO/ONstudyABC' had non-zero exit status

--- failed re-building 'OmicNavigatorAPI.Rnw'

--- re-building 'OmicNavigatorUsersGuide.Rnw' using Sweave
Installing study "vignetteExample" in C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/OmicNavigator/tmp/RtmpIVyUfO/file3744196e37cc
Exporting study "vignetteExample" as an R package
Calculating pairwise overlaps. This may take a while...
Exported study to C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\OmicNavigator\tmp\RtmpIVyUfO/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
Packages required but not available: 'broom', '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: 'dbplyr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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', 'ggfortify', 'ggplot2', 'tidyr'

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:
  'rstan', 'rstantools', 'bayesplot', 'ggplot2', 'dplyr', 'tibble',
  'tidyr', 'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'sva', 'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'tidyverse', 'readxl', 'TCGAbiolinks'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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', 'rhdf5', 'dplyr', 'Rhdf5lib'

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', 'MDSMap'

Package suggested but not available for checking: 'vcfR'

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: 'sf'

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

Package suggested but not available for checking: 'testthat'

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

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

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

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:
  'keyATM', 'tibble', 'quanteda', 'ggplot2', 'cowplot', 'dplyr', 'cli'

Packages suggested but not available for checking:
  'testthat', 'stm', 'seededlda', 'quanteda.textmodels', 'shinytest'

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/OpenCL/OpenCL.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'unix', 'haven', 'feather'
Packages required but not available: 'secr', 'RcppParallel'

Package suggested but not available for checking: 'testthat'

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

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

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

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: 'usdata', 'ggplot2', 'readr', 'tibble'

Packages suggested but not available for checking:
  'broom', 'dplyr', 'forcats', 'testthat', 'tidyr', 'tidytext'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'mlr', 'farff', 'lintr'
Packages required but not available: 'MSEtool', 'DLMtool', 'SAMtool'

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

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

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

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

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

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'plotly', 'rdrop2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'engine.R'
  Comparing 'engine.Rout' to 'engine.Rout.save' ...4d3
< Linking to: OpenSSL 1.1.1k  25 Mar 2021
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'openair'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'InterVA5', 'InSilicoVA', 'ggplot2', 'cli'

Packages suggested but not available for checking: 'nbc4va', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'opera-vignette.Rmd' using rmarkdown
Loading required package: nlme
This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.
Quitting from lines 106-109 (./../inst/rmd/example.Rmd) 
Quitting from lines 25-27 (./../inst/rmd/example.Rmd) 
Error: processing vignette 'opera-vignette.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building 'opera-vignette.Rmd'

SUMMARY: processing the following file failed:
  'opera-vignette.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # testthat.R -- automated test cases
  > #
  > # MS
  > # Created: August 8, 2020
  > 
  > 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("OptCirClust")
  Loading required package: OptCirClust
  > require("Ckmeans.1d.dp")
  Loading required package: Ckmeans.1d.dp
  > 
  > test_check("OptCirClust")
  Error in test_check("OptCirClust") : could not find function "test_check"
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'CircularGenomes.Rmd' using rmarkdown
--- finished re-building 'CircularGenomes.Rmd'

--- re-building 'Performance.Rmd' using rmarkdown
Quitting from lines 17-111 (Performance.Rmd) 
Error: processing vignette 'Performance.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Performance.Rmd'

--- re-building 'Tutorial_CirClust.Rmd' using rmarkdown
--- finished re-building 'Tutorial_CirClust.Rmd'

--- re-building 'Tutorial_FramedClust.Rmd' using rmarkdown
--- finished re-building 'Tutorial_FramedClust.Rmd'

SUMMARY: processing the following file failed:
  'Performance.Rmd'

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

Packages suggested but not available for checking:
  'cowplot', 'ggrepel', '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', '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', 'fields'

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 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'
Error(s) in re-building vignettes:
--- re-building 'ocs-vignette.Rmd' using rmarkdown
--- finished re-building 'ocs-vignette.Rmd'

--- re-building 'ped-vignette.Rmd' using rmarkdown
Warning in kinship2::pedigree(id = Pedig$Indiv, dadid = Pedig$Sire, momid = Pedig$Dam,  :
  More than 25% of the gender values are 'unknown'
Quitting from lines 119-122 (ped-vignette.Rmd) 
Error: processing vignette 'ped-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ped-vignette.Rmd'

--- re-building 'seg-vignette.Rmd' using rmarkdown
--- finished re-building 'seg-vignette.Rmd'

SUMMARY: processing the following file failed:
  'ped-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'arm'

Package which this enhances but not available for checking: 'haven'
Running 'exporting-methods.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespaces in Imports field not imported from:
  'boot' 'splines'
  All declared Imports should be used.
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.
Packages suggested but not available for checking: 'caret', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'ordinalClust.Rmd' using rmarkdown

Attaching package: 'ordinalClust'

The following object is masked from 'package:graphics':

    plot

The following objects are masked from 'package:base':

    plot, summary

Quitting from lines 63-82 (ordinalClust.Rmd) 
Error: processing vignette 'ordinalClust.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ordinalClust.Rmd'

SUMMARY: processing the following file failed:
  'ordinalClust.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'verification'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'rms'
Packages required but not available: 'ggthemes', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'microplot'
Packages suggested but not available for checking: 'testthat', 'forecast'
Error(s) in re-building vignettes:
--- re-building 'generalizedCV.Rmd' using rmarkdown
Quitting from lines 282-317 (generalizedCV.Rmd) 
Error: processing vignette 'generalizedCV.Rmd' failed with diagnostics:
there is no package called 'forecast'
--- failed re-building 'generalizedCV.Rmd'

SUMMARY: processing the following file failed:
  'generalizedCV.Rmd'

Error: Vignette re-building failed.
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.
Packages required but not available: 'googleAuthR', 'googleCloudVisionR'

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

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', 'lintr'

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

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

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

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'R6' 'openssl'
  All declared Imports should be used.
Packages required but not available: 'janitor', 'sf', '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', '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:
  'testthat', 'epicontacts'

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:

> ### 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
Packages suggested but not available for checking:
  'dplyr', 'forcats', 'ggplot2', 'testthat', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'intro-to-outcomerate.Rmd' using rmarkdown
Quitting from lines 29-34 (intro-to-outcomerate.Rmd) 
Error: processing vignette 'intro-to-outcomerate.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'intro-to-outcomerate.Rmd'

SUMMARY: processing the following file failed:
  'intro-to-outcomerate.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'outRanger.Rmd' using rmarkdown
Quitting from lines 120-127 (outRanger.Rmd) 
Error: processing vignette 'outRanger.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'outRanger.Rmd'

SUMMARY: processing the following file failed:
  'outRanger.Rmd'

Error: Vignette re-building failed.
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', 'memisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: '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: 'devtools', 'pkgload', 'tibble', 'cli'

Package suggested but not available for checking: 'testthat'

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

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'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'twang', 'EnvStats', 'devtools', 'dplyr', 'ggplot2', 'ggrepel',
  'metR', 'tibble'

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: 'leaflet', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggridges'
Error(s) in re-building vignettes:
--- re-building 'basic-usage.Rmd' using rmarkdown
Quitting from lines 24-31 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'basic-usage.Rmd'

SUMMARY: processing the following file failed:
  'basic-usage.Rmd'

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

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

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

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

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

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: 'ggplot2', 'pkgsearch', 'sugrrants'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'pkgbuild', 'pkgload', 'rcmdcheck', 'rhub'

Packages suggested but not available for checking:
  'cleanr', 'devtools', 'document', 'lintr', 'rasciidoc', 'roxygen2',
  'testthat', 'usethis'

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

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', 'flexsurv', 'survminer', 'systemfit', 'IPDFileCheck',
  'valueEQ5D', 'car', 'ggplot2', 'broom', 'tidyverse', 'tibble',
  'dplyr', 'tidyr', 'haven'

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'ape'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'e1071'
  All declared Imports should be used.
Packages required but not available: 'genbankr', 'GenomicAlignments'

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', 'tidyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'pagemap.Rmd' using rmarkdown
Quitting from lines 20-29 (pagemap.Rmd) 
Error: processing vignette 'pagemap.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'pagemap.Rmd'

SUMMARY: processing the following file failed:
  'pagemap.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in 'pagenum-Ex.R' failed
The error most likely occurred in:

> ### Name: pagenum
> ### Title: Put Page Numbers on Graphics
> ### Aliases: pagenum setPagenum getPagenum
> 
> ### ** Examples
> 
> # base graphics
> setPagenum(1)
> plot(Sepal.Length~Sepal.Width, data=iris, col=Species, pch=19)
> pagenum()
> 
> # lattice, date
> setPagenum(getPagenum()+1) # Manual increment
> require(lattice)
Loading required package: lattice
> xyplot(Sepal.Length~Sepal.Width, data=iris, groups=Species)
> pagenum(date=TRUE)
> 
> # ggplot2, top-right
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
> ggplot(iris, aes(x=Sepal.Width, y=Sepal.Length,
+   color=Species)) + geom_point() + theme_classic()
Error in ggplot(iris, aes(x = Sepal.Width, y = Sepal.Length, color = Species)) : 
  could not find function "ggplot"
Execution halted
Error(s) in re-building vignettes:
--- re-building 'pagenum_examples.Rmd' using rmarkdown
Quitting from lines 66-71 (pagenum_examples.Rmd) 
Error: processing vignette 'pagenum_examples.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'pagenum_examples.Rmd'

SUMMARY: processing the following file failed:
  'pagenum_examples.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'WikidataR'
Package required but not available: 'sccore'

Packages suggested but not available for checking:
  'BiocParallel', 'dplyr', 'ggplot2', 'p2data', 'scde', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'alr4'
Error(s) in re-building vignettes:
--- re-building 'MultipleComparisons.Rmd' using rmarkdown
--- finished re-building 'MultipleComparisons.Rmd'

--- re-building 'PairVizIntroduction.Rmd' using rmarkdown
--- finished re-building 'PairVizIntroduction.Rmd'

--- re-building 'pcp.Rmd' using rmarkdown
Quitting from lines 131-152 (pcp.Rmd) 
Error: processing vignette 'pcp.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'pcp.Rmd'

SUMMARY: processing the following file failed:
  'pcp.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'mcprofile'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'cliapp', 'pkgbuild', 'pkgcache', 'rematch2', 'tibble'

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

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

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

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'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'agricolae', 'rworldmap'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'iterators'
  All declared Imports should be used.
Package required but not available: 'rematch2'

Packages suggested but not available for checking:
  'gameofthrones', 'ggplot2', 'ggthemes', 'harrypotter', 'testthat',
  'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'palettetown-Ex.R' failed
The error most likely occurred in:

> ### 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'
Packages suggested but not available for checking:
  'testthat', 'stars', 'viridis'
Running examples in 'palr-Ex.R' failed
The error most likely occurred in:

> ### Name: image_pal
> ### Title: Map data values to colours
> ### Aliases: image_pal image_raster image_stars
> 
> ### ** Examples
> 
> set.seed(28)
> vals <- sort(rnorm(100))
> cols <- image_pal(vals, zlim = c(-2.4, 2))
> plot(vals, col = cols); abline(h = 2)
> points(vals, pch  = 19, cex = 0.1) ## zlim excluded some of the range
> if (requireNamespace("raster", quietly = TRUE)) {
+ im <- image_raster(volcano)
+ library(raster)
+ plotRGB(im)
+ }
Loading required package: sp
Warning in .couldBeLonLat(x, warnings = warnings) :
  CRS is NA. Assuming it is longitude/latitude
> if (!requireNamespace("stars", quietly = TRUE)) {
+ library(stars)
+ x <- st_as_stars(volcano)
+ plot(image_stars(x), rgb = 1:3)
+ }
Error in library(stars) : there is no package called 'stars'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'bivariate_choropleths.Rmd' using rmarkdown
Loading required package: latticeExtra
Loading required package: lattice
Loading required package: maps
Loading required package: classInt
Loading required package: grid
Loading required package: pals
--- finished re-building 'bivariate_choropleths.Rmd'

--- re-building 'pals_examples.Rmd' using rmarkdown
Quitting from lines 323-329 (pals_examples.Rmd) 
Error: processing vignette 'pals_examples.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building 'pals_examples.Rmd'

SUMMARY: processing the following file failed:
  'pals_examples.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'FactoClass'

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

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', 'ggplot2', 'dplyr', 'tibble', 'pec'

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', 'dplyr', 'PAMmisc', 'readr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'smoothmest'
  All declared Imports should be used.
Packages required but not available:
  'rstan', 'rstantools', 'plotly', 'dplyr', 'tidyr', 'RcppParallel',
  'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'memisc', 'Epi', 'rms', 'forecast'
Packages required but not available:
  'dplyr', 'ggplot2', 'jtools', 'lmerTest', 'tibble'

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'car', 'geepack', 'skimr', 'tidyr', 'testthat'

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.
Error(s) in re-building vignettes:
--- re-building 'panta-rhei.Rmd' using rmarkdown
Quitting from lines 42-46 (panta-rhei.Rmd) 
Error: processing vignette 'panta-rhei.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'panta-rhei.Rmd'

SUMMARY: processing the following file failed:
  'panta-rhei.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'RcppParallel'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'run-all.R'
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
Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFM', 'brms', 'broom', 'car', 'cplm', 'dplyr',
  'EGAnet', 'FactoMineR', 'geepack', 'ggplot2', 'gt', 'lavaSearch2',
  'lmerTest', 'mediation', 'metaBMA', 'mice', 'M3C', 'panelr',
  'pbkrtest', 'projpred', 'rstanarm', 'see', 'sjstats', 'testthat'
Packages required but not available: 'TIMP', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'GGally', 'ggplot2', 'testthat'
Packages unavailable to check Rd xrefs: 'GGally', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'Simulating-Power.Rmd' using rmarkdown
Quitting from lines 26-34 (Simulating-Power.Rmd) 
Error: processing vignette 'Simulating-Power.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Simulating-Power.Rmd'

SUMMARY: processing the following file failed:
  'Simulating-Power.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'easyalluvial', 'tidyr', 'dplyr', 'forcats', '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:
  'd3r', 'ggplot2', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'introduction-to-parcoords-.Rmd' using rmarkdown
Quitting from lines 80-93 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
there is no package called 'd3r'
--- failed re-building 'introduction-to-parcoords-.Rmd'

SUMMARY: processing the following file failed:
  'introduction-to-parcoords-.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'hansard', 'mnis', 'dplyr', 'sf', 'readr'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'leaflet', 'cartogram', 'ggplot2', 'tibble',
  'janitor'

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.
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.
Packages required but not available:
  'cli', 'readr', 'tidyr', 'dplyr', 'tibble', 'pillar'

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', 'hardhat', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'dials', 'sparklyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'PartCensReg-Ex.R' failed
The error most likely occurred in:

> ### Name: Cens.SMN.PCR
> ### Title: Estimation and diagnostics for partially linear censored
> ###   regression models
> ### Aliases: Cens.SMN.PCR
> ### Keywords: package censored censoring diagnostic partial partially
> 
> ### ** Examples
> 
> dtawage = get(data(PSID1976,package = "AER"))
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'AER'
Calls: get -> data -> find.package
Execution halted
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'egcm'

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

Package suggested but not available for checking: 'egcm'

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

Package suggested but not available for checking: 'ggraph'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Workaround:
  > # https://github.com/hadley/testthat/issues/86
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tibble', 'ggplot2', 'tidyr'

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:
  'testthat', 'pkgbuild', 'pkgload'
Package suggested but not available for checking: 'MKmisc'
Packages required but not available: 'ggplot2', 'dplyr', 'GGally', 'plotly'

Packages suggested but not available for checking:
  'tidyverse', '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'
Error(s) in re-building vignettes:
--- re-building 'passport.Rmd' using rmarkdown
Quitting from lines 32-40 (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.
Package required but not available: 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'logger'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'pathfindR'
Packages required but not available:
  'ggplot2', 'ggraph', 'ggupset', 'msigdbr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'R6' 'glue' 'logging' 'purrr'
  All declared Imports should be used.
Packages required but not available: 'testthat', 'usethis'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'ggplot2', '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:
  'clusterProfiler', 'GenomicFeatures', 'survminer', '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:
  'clinUtils', 'ggplot2', 'cowplot', '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: 'landscapemetrics'

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

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

Package suggested but not available for checking: 'biomaRt'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'ade4'
  All declared Imports should be used.
Found the following significant warnings:
  putty/windows/winstore.c:665:38: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
  putty/windows/winstore.c:673:42: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/pbdRPC/pbdRPC.Rcheck/00install.out' for details.
Running examples in 'PBImisc-Ex.R' failed
The error most likely occurred in:

> ### Name: flu
> ### Title: Numbers of flu occurences in the 10 years period in the Poland.
> ### Aliases: flu
> ### Keywords: flu
> 
> ### ** Examples
> 
> data(flu)
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages required but not available: 'dplyr', 'textclean'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 119-144 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'test_pbo_function.R'
Running the tests in 'tests/test_pbo_function.R' failed.
Complete output:
  > # unit tests for pbo 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require(pbo)
  Loading required package: pbo
  Loading required package: lattice
  > 
  > context("Function usage")
  Error in context("Function usage") : could not find function "context"
  Execution halted
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.
Package required but not available: 'exact2x2'

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

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

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

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.
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.
Packages required but not available: 'ggplot2', 'riskRegression', 'pec'

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: 'fda.usc'

Packages suggested but not available for checking:
  'RDML', 'readxl', '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', 'cowplot'

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

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

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

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:
  'car', 'dplyr', 'ggplot2', 'splm'
Running examples in 'pder-Ex.R' failed
The error most likely occurred in:

> ### Name: DemocracyIncome
> ### Title: The Relation Between Democraty and Income
> ### Aliases: DemocracyIncome
> ### Keywords: datasets
> 
> ### ** Examples
> 
> #### Example 7-1
> 
> ## ------------------------------------------------------------------------
> 
> data("DemocracyIncome", package = "pder")
> 
> ## ------------------------------------------------------------------------
> data("DemocracyIncome", package="pder")
> set.seed(1)
> di2000 <- subset(DemocracyIncome, year == 2000,
+                  select = c("democracy", "income", "country"))
> di2000 <- na.omit(di2000)
> di2000$country <- as.character(di2000$country)
> di2000$country[- c(2,5, 23, 16, 17, 22, 71,  125, 37, 43, 44,
+                    79, 98, 105, 50, 120,  81, 129, 57, 58,99)] <- NA
> 
> library("ggplot2")
Error in library("ggplot2") : there is no package called 'ggplot2'
Execution halted
Running 'poppler.R'
  Comparing 'poppler.Rout' to 'poppler.Rout.save' ...4d3
< Using poppler version 21.04.0
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'readxl', 'tibble', 'tidyr'

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

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

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:
  'adabag', 'AmesHousing', 'caret', 'dplyr', 'testthat', 'vip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'pillar', 'testthat', 'vdiffr'
Running 'testthat.R'
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
Quitting from lines 734-750 (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: 'car', 'coefplot', 'papeR'

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

Packages suggested but not available for checking:
  'leaflet', 'leaflet.extras', 'gganimate', 'infer', 'moderndive',
  'readr', 'ggplot2', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bib2df', 'dplyr', 'tidyr', 'stevemisc'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'PeakError-Ex.R' failed
The error most likely occurred in:

> ### Name: PeakError
> ### Title: PeakError
> ### Aliases: PeakError
> 
> ### ** Examples
> 
> x <- seq(5, 85, by=5)
> peaks <- rbind(Peaks("chr2", x, x+3),
+                Peaks("chr3", c(25, 38, 57), c(33, 54, 75)),
+                Peaks("chr4", c(5, 32, 38, 65), c(15, 35, 55, 85)),
+                Peaks("chr5", c(12, 26, 56, 75), c(16, 54, 59, 85)))
> regions <- NULL
> for(chr in 1:5){
+   regions <- rbind(regions, {
+     data.frame(chrom=paste0("chr", chr),
+                chromStart=c(10, 30, 50, 70),
+                chromEnd=c(20, 40, 60, 80),
+                annotation=c("noPeaks", "peakStart", "peakEnd", "peaks"))
+   })
+ }
> err <- PeakError(peaks, regions)
> ann.colors <-
+   c(noPeaks="#f6f4bf",
+     peakStart="#ffafaf",
+     peakEnd="#ff4c4c",
+     peaks="#a445ee")
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Running examples in 'PeakSegDisk-Ex.R' failed
The error most likely occurred in:

> ### 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.
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Examples.Rnw' using knitr
Quitting from lines 94-107 (Examples.Rnw) 
Error: processing vignette 'Examples.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Examples.Rnw'

--- re-building 'Spatial_correlation.Rmd' using knitr
Quitting from lines 105-123 (Spatial_correlation.Rmd) 
Error: processing vignette 'Spatial_correlation.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Spatial_correlation.Rmd'

--- re-building 'Worst_case.Rmd' using knitr
Quitting from lines 67-99 (Worst_case.Rmd) 
Error: processing vignette 'Worst_case.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Worst_case.Rmd'

SUMMARY: processing the following files failed:
  'Examples.Rnw' 'Spatial_correlation.Rmd' 'Worst_case.Rmd'

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:

> ### 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
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'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'car', 'fields', 'georob', 'spsurvey'
Packages unavailable to check Rd xrefs: 'spsurvey', 'Hmisc', 'fields', 'car', 'georob'
Running examples in 'pedometrics-Ex.R' failed
The error most likely occurred in:

> ### Name: plotCor
> ### Title: Correlation plot
> ### Aliases: plotCor
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> cols <- c("cadmium", "copper", "lead", "zinc", "elev", "dist", "om")
> 
> # A single correlation matrix
> r <- cor(meuse[1:20, cols], use = "complete")
> r <- round(r, 2)
> plotCor(r)
Error: Package 'fields' needed for this function to work. Please install it.
Execution halted
Packages required but not available:
  'rvest', 'readxl', 'readr', 'ggplot2', 'plotly'

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.
Error(s) in re-building vignettes:
--- re-building 'pedtools.Rmd' using rmarkdown
Quitting from lines 17-23 (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
Package required but not available: 'adegenet'

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.
Namespace in Imports field not imported from: 'lhs'
  All declared Imports should be used.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'survminer'

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

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

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

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: 'dendextend', 'vcfR'
Running examples in 'perfectphyloR-Ex.R' failed
The error most likely occurred in:

> ### Name: RandIndexTest
> ### Title: Rand Index Test
> ### Aliases: RandIndexTest
> 
> ### ** Examples
> 
> 
> data(ex_hapMat_data)
> d1 <- reconstructPP(ex_hapMat_data, focalSNV = 1, minWindow = 1)
> d2 <- reconstructPP(ex_hapMat_data, focalSNV = 5, minWindow = 1)
> RandIndexTest(dend1 = d1,  dend2 = d2, k = 5, nperm = 100)
Error: Package "dendextend" needed for this function to work. Please install it.
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', 'RPESE', 'RobStatTM'
Packages unavailable to check Rd xrefs: 'Hmisc', 'car'
Running examples in 'PerformanceAnalytics-Ex.R' failed
The error most likely occurred in:

> ### 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
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', 'brms', 'car', 'cplm', 'dplyr', 'forecast', 'ggplot2',
  'mlogit', 'patchwork', 'rstanarm', 'rstantools', 'see', 'testthat'
Packages suggested but not available for checking:
  'dendextend', 'dendextendRcpp'
Running examples in 'pergola-Ex.R' failed
The error most likely occurred in:

> ### Name: maketangle
> ### Title: Create a gray scale tanglegram
> ### Aliases: maketangle
> 
> ### ** Examples
> 
> data(simTetra)
> simTetraGen <- bases2genotypes(simTetra, 4)
> rfMat <- calcRec(simTetraGen, 4)
> split <- splitChr(rfMat, nchr = 7)
> split <- sortLeafs(rfMat, split)
> map <- pullMap(rfMat, split = split)  
> dend <- map2dend(map)  
Error: dendextend needed for this function to work. Please install it.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
Quitting from lines 212-214 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'dendextend'
--- failed re-building 'my-vignette.Rmd'

SUMMARY: processing the following file failed:
  'my-vignette.Rmd'

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

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## Test `permute` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'car', 'dplyr', 'ggplot2', 'pbkrtest', 'tidyr', 'viridis'
Running examples in 'permutes-Ex.R' failed
The error most likely occurred in:

> ### Name: clusterperm.glmer
> ### Title: Cluster-based permutation tests for time series data, based on
> ###   generalized linear mixed-effects models or other 'buildmer' models.
> ###   This is an alias for 'clusterperm.lmer' provided for discoverability.
> ### Aliases: clusterperm.glmer
> 
> ### ** Examples
> 
> ## Don't show: 
> perms <- perm.glmer(Fz ~ Deviant*Session + (1|Subject),data=MMN[MMN$Time > 200 & MMN$Time < 205,],nperm=2,type='anova')
Loading required namespace: car
Failed with error:  'there is no package called 'car''
Error in pkgcheck(c("buildmer", "car")) : 
  Please install the following missing package: car
Calls: perm.glmer -> perm.lmer -> pkgcheck
Execution halted
Error(s) in re-building vignettes:
--- re-building 'buildmer.Rmd' using rmarkdown
Failed with error:  'there is no package called 'ggplot2''
Quitting from lines 62-63 (buildmer.Rmd) 
Error: processing vignette 'buildmer.Rmd' failed with diagnostics:
Please install package ggplot2
--- failed re-building 'buildmer.Rmd'

--- re-building 'permutes.Rmd' using rmarkdown
Failed with error:  'there is no package called 'ggplot2''
Quitting from lines 69-70 (permutes.Rmd) 
Error: processing vignette 'permutes.Rmd' failed with diagnostics:
Please install package ggplot2
--- 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: 'personalized'

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

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', 'badger'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'DataVisualizations', 'dplyr', 'finalfit', 'ggplot2', 'ggthemes',
  'Hmisc', 'VIM', 'mice', 'plotly', 'readr', 'readxl', 'tibble',
  'tidyr'

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:
  'readxl', 'factoextra', 'bipartite', 'smerc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'readr', 'gt', 'readxl', 'kableExtra',
  'tidyverse'
Error(s) in re-building vignettes:
--- re-building 'advanced_usage.Rmd' using rmarkdown
Quitting from lines 13-20 (advanced_usage.Rmd) 
Error: processing vignette 'advanced_usage.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'advanced_usage.Rmd'

--- re-building 'huxtable_tips.Rmd' using rmarkdown
Quitting from lines 13-20 (huxtable_tips.Rmd) 
Error: processing vignette 'huxtable_tips.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'huxtable_tips.Rmd'

--- re-building 'pharmaRTF.Rmd' using rmarkdown
Quitting from lines 13-20 (pharmaRTF.Rmd) 
Error: processing vignette 'pharmaRTF.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'pharmaRTF.Rmd'

--- re-building 'tf_from_file.Rmd' using rmarkdown
Quitting from lines 13-21 (tf_from_file.Rmd) 
Error: processing vignette 'tf_from_file.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'tf_from_file.Rmd'

SUMMARY: processing the following files failed:
  'advanced_usage.Rmd' 'huxtable_tips.Rmd' 'pharmaRTF.Rmd'
  'tf_from_file.Rmd'

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

Package suggested but not available for checking: 'BiocParallel'

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

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.
Packages suggested but not available for checking:
  'ggplot2', 'randomForestSRC'
Packages required but not available: 'dplyr', 'broom', 'tidyr', 'tibble'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr', '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: 'fields', 'car'
Packages required but not available: 'Hmisc', 'cowplot', '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', 'ggplot2', '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: 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyverse', 'tidyr', 'dplyr', 'lingtypology', 'testthat', 'readxl'
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', 'tibble', 'dplyr', 'tidyr', 'readr', 'readxl'

Packages suggested but not available for checking:
  'hyperSpec', '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'

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.
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', 'dplyr', 'tidyr'

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: 'photobiology'

Packages suggested but not available for checking:
  'photobiologyWavebands', 'ggplot2', 'ggspectra'

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', 'gunit', 'tealeaves'

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

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

Package suggested but not available for checking: 'testthat'

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

Attaching package: 'ape'

The following object is masked from 'package:phylogram':

    as.phylo

Quitting from lines 223-243 (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
Packages required but not available: 'ggplot2', 'ggraph', '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: 'clustMixType'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'PhysicalActivity-Ex.R' failed
The error most likely occurred in:

> ### 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
Packages suggested but not available for checking:
  'childsds', 'dplyr', 'ggplot2', 'lintr', 'testthat', 'tidyr'
Running 'spelling.R'
  Running 'test-all.R'
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
--- finished re-building 'Everest.Rmd'

--- re-building 'IdealWeightComparison.Rmd' using rmarkdown
Quitting from lines 16-43 (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 (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: 'tibble'

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

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

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

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

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

Packages suggested but not available for checking:
  'DiagrammeR', 'dplyr', 'ggplot2', 'nycflights13', 'testthat',
  'tibble'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'sf', 'tidyverse', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'pinochet.Rmd' using rmarkdown
Quitting from lines 52-58 (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
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ##
  > ## [testthat.r]
  > ##
  > ## author     : Ed Goodwin
  > ## project    : pipefittr
  > ## createdate : 05.07.2016
  > ##
  > ## description:
  > ##    test scaffolding for pipefittr
  > ##    run tests with devtools::test() in R console
  > ##
  > ## version: 0.01
  > ## changelog:
  > ##
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'modelr', 'tidyverse'
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
Quitting from lines 119-141 (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
Packages suggested but not available for checking:
  'testthat', 'devtools', 'hdrcde'
Package required but not available: 'ggplot2'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'pivotaltrackR.Rmd' using rmarkdown
Quitting from lines 12-15 (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
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'basictabler', '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 required but not available: 'broom'

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: 'cli', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'pkgbuild', 'pkgcache', 'rematch2', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rematch2', 'tibble'

Packages suggested but not available for checking:
  'leaflet', 'pkgload', 'testthat'

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

Package suggested but not available for checking: 'sna'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'testthat'
Package unavailable to check Rd xrefs: 'pkgdown'
Packages required but not available: 'parsedate', 'tibble'

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

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

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

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

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:

> ### 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 (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
Packages suggested but not available for checking:
  'BayesMallows', 'PLMIX', 'StatRank', 'kableExtra', 'testthat'
Package unavailable to check Rd xrefs: 'BayesMallows'
Package required but not available: 'ggplot2'

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: 'sf'

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

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

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

Package suggested but not available for checking: 'lintr'

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

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.
Error(s) in re-building vignettes:
--- re-building 'testing-platowork.Rmd' using rmarkdown
Quitting from lines 59-75 (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: 'mnlogit'

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', 'ggforce', 'ggrepel', 'cowplot', 'UpSetR', 'dplyr'

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: 'ggplot2', 'ggmcmc', 'StatRank'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'AER', 'car', 'clusterSEs', 'spdep', 'splm', 'Ecdat'
Packages unavailable to check Rd xrefs: 'AER', 'car'
Error(s) in re-building vignettes:
--- re-building 'A_plmPackage.Rmd' using rmarkdown
Quitting from lines 1895-1897 (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
Version:  1.37.5
Date:     2020-06-17
Author:   Philip Leifeld (University of Essex)

Consider submitting praise using the praise or praise_interactive functions.
Please cite the JSS article in your publications -- see citation("texreg").
--- finished re-building 'B_plmFunction.Rmd'

--- re-building 'C_plmModelComponents.Rmd' using rmarkdown
Quitting from lines 164-165 (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: 'dplyr', 'tidyr', 'ggplot2'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'gganimate', 'ggnewscale', 'ggplot2', 'rerddap', 'sf',
  '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: 'ggplot2', 'ggfittext'

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

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

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

Packages suggested but not available for checking:
  'ggthemes', 'GGally', 'testthat', 'devtools', 'shinytest', 'vdiffr',
  'broom', 'dendextend', 'sf', 'IRdisplay', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'scape'
Packages required but not available: 'ggplot2', 'dplyr', 'patchwork'

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:
  'mixOmics', 'plsgenomics', 'SensoMineR'
Running examples in 'PLSbiplot1-Ex.R' failed
The error most likely occurred in:

> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: 'pls'

The following object is masked from 'package:stats':

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'mixOmics'
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Packages suggested but not available for checking: 'FactoMineR', 'plspm'
Packages required but not available:
  'parsnip', 'tibble', 'mixOmics', '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: 'plsRglm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test_import.R'
  Running 'test_library.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'plsRglm', 'mixOmics', '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.
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.
Namespace in Imports field not imported from: 'ssh'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'testthat', 'readr', 'feather', 'mockery'
Packages unavailable to check Rd xrefs: 'readr', 'feather'
Packages required but not available: 'bupaR', 'petrinetR'

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: 'car', 'NSM3'
Package unavailable to check Rd xrefs: 'NSM3'
Packages required but not available: 'dplyr', 'pillar', 'tidyr', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: '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', '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:
  'caret', 'forecast', 'randomForestSRC', 'rattle', 'testthat'
Running examples in 'pmml-Ex.R' failed
The error most likely occurred in:

> ### Name: pmml.ARIMA
> ### Title: Generate PMML for an ARIMA object the *forecast* package.
> ### Aliases: pmml.ARIMA
> 
> ### ** Examples
> 
> library(forecast)
Error in library(forecast) : there is no package called 'forecast'
Execution halted
Packages required but not available: 'dplyr', 'ggplot2'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'abc' 'doParallel' 'gdistance' 'geosphere' 'lhs' 'metRology' 'raster'
  'trend'
  All declared Imports should be used.
Package required but not available: 'PUlasso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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', 'cli', 'dplyr', 'dbplyr', 'gt', 'testthat', 'tibble',
  'tidyr'

Packages suggested but not available for checking:
  'ggforce', 'ggplot2', 'readr', 'sparklyr', 'dittodb'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'devtools', '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: 'parsnip', 'tibble', '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:
  'colourpicker', 'ggplot2', 'hexSticker'

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', 'devtools', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'DiagrammeR'
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', 'cli', 'dplyr', 'tibble', 'tidyr'

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

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

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

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

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', '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'
Error(s) in re-building vignettes:
--- re-building 'OpenCPU.Rmd' using rmarkdown
--- finished re-building 'OpenCPU.Rmd'

--- re-building 'vignette.Rmd' using rmarkdown
... activating corpus: GERMAPARLMINI (version: 0.0.1 | build date: 2019-02-23)
... activating corpus: REUTERS
Quitting from lines 123-124 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
invalid UTF-8 byte sequence detected; try calling stri_enc_toutf8()
--- 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: 'MDSMap'

Packages suggested but not available for checking:
  'ggplot2', 'Hmisc', 'updog', 'mappoly'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'Rsamtools', 'VariantAnnotation', 'GenomicFeatures', 'ggplot2',
  'adegenet'
Packages unavailable to check Rd xrefs: 'adegenet', 'Rsamtools', 'BSgenome', 'GenomicFeatures', 'VariantAnnotation'
Namespace in Imports field not imported from: 'regtools'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'Rcmdr'
Packages required but not available: 'ggplot2', '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:
  'ggplot2', 'tidyr', 'dplyr'
Running examples in 'pomp-Ex.R' failed
The error most likely occurred in:

> ### Name: bsflu
> ### Title: Influenza outbreak in a boarding school
> ### Aliases: bsflu
> 
> ### ** Examples
> 
> library(tidyr)
Error in library(tidyr) : there is no package called 'tidyr'
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:
  'testthat', 'tibble', 'dplyr', 'dbplyr'
Running examples in 'pool-Ex.R' failed
The error most likely occurred in:

> ### Name: dplyr-db-methods
> ### Title: DBIConnection methods from dplyr and dbplyr
> ### Aliases: dplyr-db-methods copy_to.Pool tbl.Pool db_analyze.Pool
> ###   db_begin.Pool db_commit.Pool db_create_index.Pool
> ###   db_create_indexes.Pool db_create_table.Pool db_data_type.Pool
> ###   db_desc.Pool db_drop_table.Pool db_explain.Pool db_has_table.Pool
> ###   db_insert_into.Pool db_list_tables.Pool db_query_fields.Pool
> ###   db_query_rows.Pool db_rollback.Pool db_save_query.Pool
> ###   db_write_table.Pool sql_escape_string.Pool sql_join.Pool
> ###   sql_select.Pool sql_semi_join.Pool sql_subquery.Pool
> ###   sql_translate_env.Pool db_collect.Pool db_compute.Pool
> ###   db_sql_render.Pool sql_escape_logical.Pool sql_join_suffix.Pool
> 
> ### ** Examples
> 
> if (requireNamespace("RSQLite", quietly = TRUE)) {
+   library(dplyr)
+ 
+   db <- tempfile()
+   pool <- dbPool(RSQLite::SQLite(), dbname = db)
+ 
+   # copy a table into the database
+   copy_to(pool, mtcars, "mtcars", temporary = FALSE)
+ 
+   # retrieve a table
+   mtcars_db <- tbl(pool, "mtcars")
+   mtcars_db
+   mtcars_db %>% select(mpg, cyl, disp)
+   mtcars_db %>% filter(cyl == 6) %>% collect()
+ 
+   poolClose(pool)
+ } else {
+   message("Please install the 'RSQLite' package to run this example")
+ }
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Running 'testthat.r'
Running the tests in 'tests/testthat.r' failed.
Complete output:
  > ### 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', 'rstantools', 'brms', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'pkgdown', 'roxygen2'
Packages required but not available: 'ggplot2', 'dplyr', 'tibble'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Errors in running code in vignettes:
when running code in 'burkina-faso-females.Rnw'

> options(width = 70, continue = " ", SweaveHooks = list(fig = function() par(mar = c(5.1, 
+     4.1, 1.1, 2.1))))

> pdf.options(pointsize = 9)

> library(reshape)

> library(ggplot2)

  When sourcing 'burkina-faso-females.R':
Error: there is no package called 'ggplot2'
Execution halted

  'burkina-faso-females.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
--- re-building 'burkina-faso-females.Rnw' using Sweave

Error: processing vignette 'burkina-faso-females.Rnw' failed with diagnostics:
 chunk 1 (label = sweave-setup) 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'burkina-faso-females.Rnw'

SUMMARY: processing the following file failed:
  'burkina-faso-females.Rnw'

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

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 unavailable to check Rd xrefs: 'rags2ridges', 'ragt2ridges'
Packages required but not available:
  'dplyr', 'forecast', 'timetk', 'tibble'

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

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'

Package suggested but not available for checking: 'car'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'bslib'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
Quitting from lines 66-74 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
`map_df()` requires dplyr
--- failed re-building 'Introduction.Rmd'

SUMMARY: processing the following file failed:
  'Introduction.Rmd'

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

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

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

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

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.
Packages required but not available: 'tibble', '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: 'sf'

Packages suggested but not available for checking: 'lwgeom', 'cartography'

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

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

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:
  'readr', 'tibble', 'dplyr', 'tidyr', 'naniar'

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

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'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'factoextra'
Package unavailable to check Rd xrefs: 'advclust'
Error(s) in re-building vignettes:
--- re-building 'fcm.Rmd' using rmarkdown
Quitting from lines 45-48 (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 (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', 'leaflet', 'PakPC2017', 'tidyr', 'tmap'

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:
  'GGally', 'ggplot2', 'roxygen2', 'PPtreeViz'

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

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', 'readxl'

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: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Packages suggested but not available for checking: 'spdep', 'spatialreg'
Package suggested but not available for checking: 'doBy'
Namespaces in Imports field not imported from:
  'lmtest' 'sandwich'
  All declared Imports should be used.
Packages required but not available: 'precrec', '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', 'ggplot2', 'tibble', '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'
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 (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: 'escalation', 'dplyr', 'kableExtra'

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', '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', 'tidyr'

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

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

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

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

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', 'mclogit', 'mlogit', 'sampleSelection'
Packages unavailable to check Rd xrefs: 'AER', 'caret', 'mclogit', 'sampleSelection'
Running 'testthat-prediction.R'
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
Packages required but not available: 'ggplot2', 'pbkrtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'rattle', 'adabag', 'colourpicker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'rpart'
  All declared Imports should be used.
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', 'spdep'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'prepplotOverview.Rmd' using rmarkdown
Quitting from lines 31-64 (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
Packages required but not available: 'psycho', 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'Hmisc', 'testthat', 'shinytest'
Running 'presize.R'
Running the tests in 'tests/presize.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:
  'lintr', 'testthat', 'vdiffr'
Packages required but not available:
  'broom', 'car', 'dplyr', 'forcats', 'kableExtra', 'plotly', 'tibble',
  'tidycat', 'tidyr', 'vip'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'prettymapr-Ex.R' failed
The error most likely occurred in:

> ### Name: mergebbox
> ### Title: Combine bounding boxes
> ### Aliases: mergebbox
> 
> ### ** Examples
> 
> box1 <- searchbbox("wolfville, ns")
Using default API key for pickpoint.io. If batch geocoding, please get your own (free) API key at https://app.pickpoint.io/sign-up
Error: $ operator is invalid for atomic vectors
Execution halted
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tibble'

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', 'reclin', 'caret'

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'bipartite', 'cowplot', 'DiagrammeR'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', '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:
  'sf', 'dplyr', 'rnaturalearth', 'rvest', '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', 'ggnewscale', 'ggtext', 'dplyr', 'Hmisc'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'LaplacesDemon' 'epitools' 'rpivotTable' 'shiny' 'shinyMatrix'
  All declared Imports should be used.
Packages required but not available:
  'bupaR', 'processmapR', 'dplyr', 'tidyr', 'DiagrammeR'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'bupaR', 'edeaR', 'DiagrammeR', 'ggplot2', 'ggthemes',
  'forcats', 'plotly', 'tidyr'

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:
  'dplyr', 'ggplot2', 'ggrepel', 'rrtable', 'tidyr', 'predict3d',
  'interactions'

Package suggested but not available for checking: 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'output.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'ggplot2'
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.
Packages required but not available: 'cli', 'profile'

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:
  'dm', 'DiagrammeR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following sources/headers not terminated with a newline:
  src/libprofit/include/profit/config.h
Some compilers warn on such files.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(ProfoundData)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'devtools'
Running 'manual-test-source.R'
  Running 'manual-tests.R'
  Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'GeneralizedUmatrix', 'plotly'

Packages suggested but not available for checking:
  'DataVisualizations', 'spdep', 'fields', 'dendextend',
  'DatabionicSwarm', 'parallelDist'

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:
  'dplyr', 'readr', 'sessioninfo', 'tibble'

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', 'qs', 'ggplot2', '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', 'reprex', 'testthat', 'tidyr'

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'RcppParallel', 'rstan', 'rstantools',
  'StanHeaders', 'tidyr'

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

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

Packages suggested but not available for checking:
  'ALDEx2', 'cccrm', 'ggdendro', 'plotly', 'SDMTools', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'kableExtra', 'testthat', 'dplyr', 'pkgdown'
Error(s) in re-building vignettes:
--- re-building 'PROsetta.Rmd' using rmarkdown
Quitting from lines 23-27 (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
Packages required but not available:
  'ggplot2', 'readr', 'imputeTS', 'torch', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  WARNING: failed to apply patch patches/CRAN/protolite.diff
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/protolite/protolite.Rcheck/00install.out' for details.
Packages required but not available:
  'dplyr', 'janitor', 'tidyr', 'ggplot2', 'forcats', 'tibble',
  'plotly', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'dendextend', 'heatmaply', 'viridis', 'drc', 'naniar'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rdtLite', 'rdt', 'testthat'
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'rdtLite', 'rdt', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'rdt', 'rdtLite', 'testthat'
Packages suggested but not available for checking: 'rdt', 'rdtLite'
Package suggested but not available for checking: 'foghorn'
Running 'all_tests.R'
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
Package required but not available: 'wavScalogram'

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

> ### 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 (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 (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: 'PogromcyDanych'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'pscl-Ex.R' failed
The error most likely occurred in:

> ### 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
Errors in running code in vignettes:
when running code in 'countreg.Rnw'

> library("sandwich")

> library("lmtest")
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


> library("MASS")

> library("car")

  When sourcing 'countreg.R':
Error: there is no package called 'car'
Execution halted

  'countreg.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'countreg.Rnw' using Sweave
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Error: processing vignette 'countreg.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("car") : there is no package called 'car'

--- failed re-building 'countreg.Rnw'

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

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

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: 'testthat'

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

Package suggested but not available for checking: 'sensitivity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'simulation-study.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 403-408 (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', 'tidyr',
  'tibble', 'miceadds', '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: 'dplyr'

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

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

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'

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

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

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

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

Packages suggested but not available for checking:
  'bib2df', 'cli', 'testthat'

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

Packages suggested but not available for checking:
  'semPlot', 'graphicalVAR', 'metaSEM', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'likert'
Packages required but not available: 'broom', 'cli', 'dplyr', 'ez'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
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:
  'dplyr', 'ggplot2', 'lmerTest', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'cowplot', 'ggrepel', 'interactions', 'qqplotr', 'roxygen2', 'see',
  'semPlot', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'illustrationBONDS.Rmd' using rmarkdown
Quitting from lines 32-46 (illustrationBONDS.Rmd) 
Error: processing vignette 'illustrationBONDS.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'illustrationBONDS.Rmd'

--- re-building 'illustrationSNP.Rmd' using rmarkdown
Quitting from lines 33-46 (illustrationSNP.Rmd) 
Error: processing vignette 'illustrationSNP.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'illustrationSNP.Rmd'

SUMMARY: processing the following files failed:
  'illustrationBONDS.Rmd' 'illustrationSNP.Rmd'

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

Package suggested but not available for checking: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'yaml'
  All declared Imports should be used.
Running examples in 'psyverse-Ex.R' failed
The error most likely occurred in:

> ### 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'
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 suggested but not available for checking:
  'ProjectTemplate', 'testthat'
Package suggested but not available for checking: 'plotly'
Package required but not available: 'tibble'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggformula', 'car', 'dplyr', 'Epi', 'ggplot2', 'Hmisc', 'moonBook',
  'sjmisc', 'sjPlot', 'tibble'

Packages suggested but not available for checking:
  'broom', 'GGally', 'ggfortify', 'ggpubr', 'ggsci', 'haven', 'jtools',
  'mosaic', 'rms', 'tidyverse'

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

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:

> ### 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
Packages suggested but not available for checking: 'network', 'testthat'
Running 'testthat.R'
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
Error(s) in re-building vignettes:
--- re-building 'other-criteria.Rmd' using rmarkdown
Quitting from lines 97-121 (other-criteria.Rmd) 
Error: processing vignette 'other-criteria.Rmd' failed with diagnostics:
there is no package called 'network'
--- failed re-building 'other-criteria.Rmd'

--- re-building 'pulsar.Rmd' using rmarkdown
--- finished re-building 'pulsar.Rmd'

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

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

Package suggested but not available for checking: 'TxDb.Hsapiens.UCSC.hg19.knownGene'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'fda', 'fda.usc', 'ggplot2', 'monoClust', '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', 'ggplot2', 'fda', '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.
Running 'purged.filesizes.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'caret', 'dplyr', 'ggplot2', 'testthat', 'tibble', 'tidyr'
Running examples in 'purgeR-Ex.R' failed
The error most likely occurred in:

> ### Name: ip_op
> ### Title: Opportunity of purging
> ### Aliases: ip_op
> 
> ### ** Examples
> 
> # Original pedigree file in Gulisija & Crow (2007)
> pedigree <- tibble::tibble(
+   id = c("M", "K", "J", "a", "c", "b", "e", "d", "I"),
+   dam = c("0", "0", "0", "K", "M", "a", "c", "c", "e"),
+   sire = c("0", "0", "0", "J", "a", "J", "b", "b", "d")
+ )
Error in loadNamespace(x) : there is no package called 'tibble'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ip.Rmd' using rmarkdown
Quitting from lines 20-31 (ip.Rmd) 
Error: processing vignette 'ip.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building 'ip.Rmd'

--- re-building 'purgeR-tutorial.Rmd' using rmarkdown
Quitting from lines 20-26 (purgeR-tutorial.Rmd) 
Error: processing vignette 'purgeR-tutorial.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'purgeR-tutorial.Rmd'

SUMMARY: processing the following files failed:
  'ip.Rmd' 'purgeR-tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in 'purrr-Ex.R' failed
The error most likely occurred in:

> ### Name: cross
> ### Title: Produce all combinations of list elements
> ### Aliases: cross cross2 cross3 cross_df cross_n cross_d
> 
> ### ** Examples
> 
> # We build all combinations of names, greetings and separators from our
> # list of data and pass each one to paste()
> data <- list(
+   id = c("John", "Jane"),
+   greeting = c("Hello.", "Bonjour."),
+   sep = c("! ", "... ")
+ )
> 
> data %>%
+   cross() %>%
+   map(lift(paste))
[[1]]
[1] "John! Hello."

[[2]]
[1] "Jane! Hello."

[[3]]
[1] "John! Bonjour."

[[4]]
[1] "Jane! Bonjour."

[[5]]
[1] "John... Hello."

[[6]]
[1] "Jane... Hello."

[[7]]
[1] "John... Bonjour."

[[8]]
[1] "Jane... Bonjour."

> 
> # cross() returns the combinations in long format: many elements,
> # each representing one combination. With cross_df() we'll get a
> # data frame in long format: crossing three objects produces a data
> # frame of three columns with each row being a particular
> # combination. This is the same format that expand.grid() returns.
> args <- data %>% cross_df()
Error: The tibble package must be installed
Backtrace:
    █
 1. ├─data %>% cross_df()
 2. └─purrr::cross_df(.)
 3.   └─purrr:::check_tibble()
Execution halted
Packages required but not available:
  'readxl', '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.
Packages required but not available: 'dplyr', 'broom', '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:
  'dplyr', 'MazamaCoreUtils', 'MazamaSpatialUtils', 'ggmap', 'leaflet',
  'openair', 'readr', 'sf', 'tibble', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'dplyr', 'tidyr', 'ez', 'phia', 'afex', 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
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
Running 'debug.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'viridis', 'ggExtra', 'dplyr', 'cowplot'

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 unavailable to check Rd xrefs: 'qdap'
Packages required but not available: 'dplyr', 'gender', '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: 'Compositional', '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: 'arm', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'broom', 'devtools', 'mice'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'rmarkdown' 'stats'
  All declared Imports should be used.
Packages required but not available: 'FactoClass', 'FactoMineR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'qMRI-test.R'
Running the tests in 'tests/qMRI-test.R' failed.
Complete output:
  > library(qMRI)
  Loading required package: awsMethods
  
  Use the function setCores() to change the number of CPU cores.
  
  > dataDir <- system.file("extdata",package="qMRI")
  > #
  > #  set file names for T1w, MTw and PDw images
  > #
  > t1Names <- paste0("t1w_",1:8,".nii.gz")
  > mtNames <- paste0("mtw_",1:6,".nii.gz")
  > pdNames <- paste0("pdw_",1:8,".nii.gz")
  > t1Files <- file.path(dataDir, t1Names)
  > mtFiles <- file.path(dataDir, mtNames)
  > pdFiles <- file.path(dataDir, pdNames)
  > #
  > #  file names of mask and B1 field map
  > #
  > B1File <- file.path(dataDir, "B1map.nii.gz")
  > maskFile <- file.path(dataDir, "mask.nii.gz")
  > #
  > #  Acquisition parameters (TE, TR, Flip Angle) for T1w, MTw and PDw images
  > #
  > TE <- c(2.3, 4.6, 6.9, 9.2, 11.5, 13.8, 16.1, 18.4,
  +         2.3, 4.6, 6.9, 9.2, 11.5, 13.8,
  +         2.3, 4.6, 6.9, 9.2, 11.5, 13.8, 16.1, 18.4)
  > TR <- rep(25, 22)
  > FA <- c(rep(21, 8), rep(6, 6), rep(6, 8))
  > #
  > #   read MPM example data
  > #
  > library(qMRI)
  > mpm <- readMPMData(t1Files, pdFiles, mtFiles,
  +                    maskFile, TR = TR, TE = TE,
  +                    FA = FA, verbose = FALSE)
  > #
  > #  Estimate Parameters in the ESTATICS model
  > #
  > modelMPM <- estimateESTATICS(mpm, method = "NLR", verbose=FALSE)
  > #
  > #  smooth maps of ESTATICS Parameters
  > #
  > setCores(2, reprt = FALSE)
  > modelMPMsp1 <- smoothESTATICS(modelMPM,
  +                               kstar = 16,
  +                               alpha = 0.004,
  +                               patchsize=1,
  +                               verbose = FALSE)
Errors in running code in vignettes:
when running code in 'qMRI-Example.Rnw'

> options(digits = 3)

> dataDir <- system.file("extdata", package = "qMRI")

> t1Names <- paste0("t1w_", 1:8, ".nii.gz")

> mtNames <- paste0("mtw_", 1:6, ".nii.gz")

> pdNames <- paste0("pdw_", 1:8, ".nii.gz")

> t1Files <- file.path(dataDir, t1Names)

> mtFiles <- file.path(dataDir, mtNames)

> pdFiles <- file.path(dataDir, pdNames)

> B1File <- file.path(dataDir, "B1map.nii.gz")

> maskFile <- file.path(dataDir, "mask.nii.gz")

> TE <- c(2.3, 4.6, 6.9, 9.2, 11.5, 13.8, 16.1, 18.4, 
+     2.3, 4.6, 6.9, 9.2, 11.5, 13.8, 2.3, 4.6, 6.9, 9.2, 11.5, 
+     13.8, 16.1, 18.4)

> TR <- rep(25, 22)

> FA <- c(rep(21, 8), rep(6, 6), rep(6, 8))

> library(qMRI)
Loading required package: awsMethods

Use the function setCores() to change the number of CPU cores.


> mpm <- readMPMData(t1Files, pdFiles, mtFiles, maskFile, 
+     TR = TR, TE = TE, FA = FA, verbose = FALSE)

> modelMPM <- estimateESTATICS(mpm, method = "NLR", 
+     verbose = FALSE)

> setCores(2, reprt = FALSE)

> modelMPMQLsp1 <- smoothESTATICS(modelMPM, mpmData = extract(mpm, 
+     "ddata"), kstar = 16, alpha = 0.004, patchsize = 1, verbose = FALSE)

... incomplete output.  Crash?

  'qMRI-Example.Rnw'... failed to complete the test
Error(s) in re-building vignettes:
--- re-building 'qMRI-Example.Rnw' using Sweave
Loading required package: awsMethods

Use the function setCores() to change the number of CPU cores.
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.
Packages required but not available: 'rvest', 'tidyverse', 'dplyr'

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

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: 'stringfish'

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

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.
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

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', 'ggplot2', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2', 'vdiffr'
Running 'Rmdtest.R'
  Running 'htmltest.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running 'test_io.R'
  Comparing 'test_io.Rout' to 'test_io.Rout.save' ... OK
  Running 'test_mapqtl_io.R'
  Comparing 'test_mapqtl_io.Rout' to 'test_mapqtl_io.Rout.save' ... OK
  Running 'test_qtl.R'
  Running 'test_scanonevar.R'
  Comparing 'test_scanonevar.Rout' to 'test_scanonevar.Rout.save' ... OK
  Running 'test_tidyIO.R'
  Comparing 'test_tidyIO.Rout' to 'test_tidyIO.Rout.save' ... OK
  Running 'testaugmentation.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'survminer'
Namespace in Imports field not imported from: 'MatrixModels'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'leaflet', 'sf'

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'ggplot2', 'GGally'
Error(s) in re-building vignettes:
--- re-building 'wilcox1973.Rmd' using rmarkdown
Quitting from lines 111-120 (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 required but not available:
  'caret', 'dplyr', 'ggplot2', 'ggrepel', 'readr', 'tibble', 'tidyr'

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

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'quanteda.textmodels', 'quanteda.textstats',
  'quanteda.textplots', 'stm', 'quanteda', 'tibble', 'tidytext',
  'ggplot2'

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

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

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

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

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

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', 'kableExtra', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'QuantileNPCI.Rmd' using rmarkdown
Quitting from lines 35-38 (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
Namespace in Imports field not imported from: 'SparseM'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'pillar', 'dplyr', 'tidyr', 'testthat'
Packages suggested but not available for checking:
  'GGally', 'ggplot2', 'network', 'sna'
Running examples in 'QuantNorm-Ex.R' failed
The error most likely occurred in:

> ### 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
Packages suggested but not available for checking:
  'testthat', 'usethis', 'vdiffr'
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.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'fastshp', '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.
Packages suggested but not available for checking: 'spider', 'adegenet'
Running examples in 'quiddich-Ex.R' failed
The error most likely occurred in:

> ### Name: changesAA
> ### Title: Identification of diagnostic molecular characters in a
> ###   nucleotide alignment that also cause diagnostic characters in the
> ###   corresponding amino acid alignment
> ### Aliases: changesAA
> 
> ### ** Examples
> 
> #using a dataset from spider
> #install.packages("spider")
> library(spider)
Error in library(spider) : there is no package called 'spider'
Execution halted
Running examples in 'quRan-Ex.R' failed
The error most likely occurred in:

> ### Name: quran_ar
> ### Title: The text of the Qur'an (Arabic, all vowels)
> ### Aliases: quran_ar
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # See first few rows
> head(quran_ar)
  surah_id ayah_id surah_title_ar surah_title_en surah_title_en_trans
1        1       1        الفاتحة     Al-Faatiha          The Opening
2        1       2        الفاتحة     Al-Faatiha          The Opening
3        1       3        الفاتحة     Al-Faatiha          The Opening
4        1       4        الفاتحة     Al-Faatiha          The Opening
5        1       5        الفاتحة     Al-Faatiha          The Opening
6        1       6        الفاتحة     Al-Faatiha          The Opening
  revelation_type                   text surah ayah ayah_title juz manzil page
1          Meccan ﻿بِسْمِ اللَّهِ الرَّحْمَٰنِ الرَّحِيمِ     1    1        1:1   1      1    1
2          Meccan  الْحَمْدُ لِلَّهِ رَبِّ الْعَالَمِينَ     1    2        1:2   1      1    1
3          Meccan          الرَّحْمَٰنِ الرَّحِيمِ     1    3        1:3   1      1    1
4          Meccan         مَالِكِ يَوْمِ الدِّينِ     1    4        1:4   1      1    1
5          Meccan إِيَّاكَ نَعْبُدُ وَإِيَّاكَ نَسْتَعِينُ     1    5        1:5   1      1    1
6          Meccan  اهْدِنَا الصِّرَاطَ الْمُسْتَقِيمَ     1    6        1:6   1      1    1
  hizb_quarter sajda sajda_id sajda_recommended sajda_obligatory
1            1 FALSE       NA                NA               NA
2            1 FALSE       NA                NA               NA
3            1 FALSE       NA                NA               NA
4            1 FALSE       NA                NA               NA
5            1 FALSE       NA                NA               NA
6            1 FALSE       NA                NA               NA
> 
> # How many ayahs are in each surah?
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Running examples in 'QZ-Ex.R' failed
The error most likely occurred in:

> ### 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
Namespaces in Imports field not imported from:
  'pracma' 'zoo'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'R2admb.Rnw' using knitr
Quitting from lines 106-111 (R2admb.Rnw) 
Error: processing vignette 'R2admb.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'R2admb.Rnw'

SUMMARY: processing the following file failed:
  'R2admb.Rnw'

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: 'fields'
Package required but not available: 'devtools'

Package suggested but not available for checking: 'ReGenesees'

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:
  'r2dii.match', 'roxygen2', 'testthat'

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

Packages suggested but not available for checking:
  'r2dii.analysis', 'r2dii.match', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'lmerTest', 'pbkrtest', 'ggplot2', 'afex', '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: 'broomExtra', '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: 'memisc', 'broom', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'caret', 'mlr'
Packages suggested but not available for checking:
  'tidyr', 'devtools', 'dplyr', 'testthat', 'ggplot2'
Running examples in 'r2rtf-Ex.R' failed
The error most likely occurred in:

> ### Name: nrow_paragraph
> ### Title: Calculate Number of Rows for a Paragraph
> ### Aliases: nrow_paragraph
> 
> ### ** Examples
> 
> library(dplyr) #required for running example
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Package unavailable to check Rd xrefs: 'BRugs'
Packages suggested but not available for checking:
  'colourpicker', 'testthat'
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'sensitivity', 'dplyr', 'ggplot2'
Packages suggested but not available for checking: 'pkgdown', 'testthat'
Packages required but not available:
  'ggplot2', 'dplyr', 'plotly', 'cowplot', 'dendextend', 'ggdendro',
  'alakazam', 'tigger', 'tidyr'

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

Packages suggested but not available for checking: 'batchelor', 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'preparingData.Rmd' using rmarkdown
Quitting from lines 28-32 (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:
  'ggplot2', 'lmerTest', 'tidyr', 'dplyr', 'Hmisc', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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', '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', 'tidyr', 'dplyr', 'tibble', 'broom', 'car', 'readr',
  'readxl', 'plotly', 'shinyFiles', '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', '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',
  'tidyr', 'dplyr', 'DiagrammeR', 'ggrepel', 'broom', 'patchwork',
  'pdp'

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', '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.
Package required but not available: 'lexicon'

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', 'dplyr', 'ggthemes'

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: 'tidyr', 'cytofan'

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

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: 'rags2ridges'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'ragtop_convertibles_in_r.Rmd' using rmarkdown
Quitting from lines 20-33 (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:
  'pegas', 'ggplot2', 'ggtree', 'scatterpie', 'phylobase', 'haplotypes'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'quanteda', 'quanteda.textstats',
  'dendextend', 'ggwordcloud'

Packages suggested but not available for checking:
  'testthat', 'quanteda.textmodels'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'intro-to-altmetric.Rmd' using rmarkdown
Quitting from lines 24-40 (intro-to-altmetric.Rmd) 
Error: processing vignette 'intro-to-altmetric.Rmd' failed with diagnostics:
`pmap_dfr()` requires dplyr
--- failed re-building 'intro-to-altmetric.Rmd'

SUMMARY: processing the following file failed:
  'intro-to-altmetric.Rmd'

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

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

Package suggested but not available for checking: 'xcms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test_all.R'
Running the tests in 'tests/test_all.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'cli', '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', 'plotly'
Error(s) in re-building vignettes:
--- re-building 'Intro-to-RaMS.Rmd' using rmarkdown
Quitting from lines 105-107 (Intro-to-RaMS.Rmd) 
Error: processing vignette 'Intro-to-RaMS.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'Intro-to-RaMS.Rmd'

--- re-building 'RaMS-and-friends.Rmd' using rmarkdown
--- finished re-building 'RaMS-and-friends.Rmd'

SUMMARY: processing the following file failed:
  'Intro-to-RaMS.Rmd'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'RandomForestsGLS_user_guide.Rmd' using rmarkdown
Warning in BRISC_estimation(coords, x = matrix(1, n, 1), y = rf_residual,  :
  The ordering of inputs x (covariates) and y (response) in BRISC_estimation has been changed BRISC 1.0.0 onwards.
Please check the new documentation with ?BRISC_estimation.
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Quitting from lines 153-170 (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 suggested but not available for checking:
  'dplyr', 'blockTools', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'randomizr_vignette.Rmd' using rmarkdown
Quitting from lines 358-376 (randomizr_vignette.Rmd) 
Error: processing vignette 'randomizr_vignette.Rmd' failed with diagnostics:
there is no package called 'blockTools'
--- failed re-building 'randomizr_vignette.Rmd'

SUMMARY: processing the following file failed:
  'randomizr_vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'toOrdinal'

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

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: 'sf', 'exactextractr'

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

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

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

Packages suggested but not available for checking:
  'BIEN', 'biomod2', 'ecospat', 'googlesheets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'rankhazard-Ex.R' failed
The error most likely occurred in:

> ### 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
Running examples in 'rankUncertainty-Ex.R' failed
The error most likely occurred in:

> ### Name: plotIntervals
> ### Title: Plot intervals
> ### Aliases: plotIntervals
> 
> ### ** Examples
> 
> intervals <- generateIntervals(10)
> p <- plotIntervals(intervals)
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: plotIntervals ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'devtools', 'gistr', 'readr', 'RMariaDB'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  datetime.c:724:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:725:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:763:3: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:971:6: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1115:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1116:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1199:7: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RApiDatetime/RApiDatetime.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'jsonlite'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'bigsnpr', 'coloc'

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

Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg19'

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

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'

Packages suggested but not available for checking:
  'roxygen2', 'dplyr', 'gurobi', '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:
  'devtools', 'goodpractice', 'lintr', 'roxygen2', 'testthat',
  'usethis'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'rare-vignette.Rmd' using rmarkdown
Quitting from lines 276-279 (rare-vignette.Rmd) 
Error: processing vignette 'rare-vignette.Rmd' failed with diagnostics:
there is no package called 'dendextend'
--- failed re-building 'rare-vignette.Rmd'

SUMMARY: processing the following file failed:
  'rare-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: 'arm'
Package required but not available: 'document'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'rasterList_fitdistr.R'
Running the tests in 'tests/rasterList_fitdistr.R' failed.
Complete output:
  > # This is a test script for rasterList function
  > # 
  > # Author: Emanuele Cordano
  > ###############################################################################
  > rm(list=ls())
  > 
  > library(rasterList)
  Loading required package: raster
  Loading required package: sp
  > library(lmom)
  > 
  > 
  > 
  > ## TESTING R CODE: 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'lintr', 'pkgdown', 'testthat'
Packages suggested but not available for checking:
  'sf', 'fields', 'exactextractr'
Packages suggested but not available for checking: 'ggplot2', 'sf'
Packages required but not available: 'ggplot2', 'Rirt'

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', 'RcppParallel', 'rstan', 'rstantools', 'StanHeaders'

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', 'dbplyr', 'testthat', 'tibble', 'vroom'
Running examples in 'RAthena-Ex.R' failed
The error most likely occurred in:

> ### 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
Package suggested but not available for checking: 'rattle'
Packages required but not available: 'tibble', 'ggplot2', 'tidyr', 'dplyr'

Packages suggested but not available for checking:
  'arulesViz', 'biclust', 'doBy', 'ggdendro', 'ggraptR', 'Hmisc',
  'mice', 'readxl', 'rggobi', 'verification'

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

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'devtools', 'weathercan', 'tidyhydat'

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

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', 'nycflights13', 'randomNames', 'readr', 'readxl', 'tibble',
  'tidyr'
Packages required but not available: 'rvest', '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: 'sf', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'viridis', 'ggplot2', 'sf', 'rayrender'
Packages suggested but not available for checking: 'pkgload', 'testthat'
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'forcats', 'sf'

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

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

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

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

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

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

Packages suggested but not available for checking: 'rhdf5', 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Rblpapi/Rblpapi.Rcheck/00install.out' for details.
Found the following non-empty subdirectories of 'inst' also used by R:
  inst/libs
It is recommended not to interfere with package subdirectories used by
R.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/blpapi_versioninfo.h
Some Unix compilers require LF line endings.
Packages required but not available: 'readxl', 'rvest'

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

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

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

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

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

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', 'sf'

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

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:
  'checkpoint', 'testthat', 'rvest'

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

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

Package suggested but not available for checking: 'car'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat_p1.R'
Running the tests in 'tests/testthat_p1.R' failed.
Complete output:
  > #testing Randy Zwitch solution
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'factoextra', 'FactoMineR', 'ggplot2'

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

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

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

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', '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', 'netmeta', 'tableone', 'readxl', 'lmerTest'

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: 'Rcmdr', 'ggplot2'

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'

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

Package suggested but not available for checking: 'car'

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: 'testthat'

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.
Packages required but not available: 'mixlm', 'phia', 'Rcmdr', 'car'

Package suggested but not available for checking: 'pbkrtest'

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

Packages suggested but not available for checking: 'qgraph', 'car', 'Hmisc'

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: 'SCVA', 'Rcmdr'

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

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.
Packages required but not available: 'RcmdrMisc', 'car'

Packages suggested but not available for checking: 'Hmisc', 'readxl', 'sem'

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', 'ggplot2', 'dplyr', 'ggtern', 'rcrossref'

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

> ### Name: cldList
> ### Title: Compact letter display for lists of comparisons
> ### Aliases: cldList
> 
> ### ** Examples
> 
> data(PoohPiglet)
> PoohPiglet$Speaker = factor(PoohPiglet$Speaker,
+                             levels=c("Pooh", "Tigger", "Piglet"))
> library(FSA)
Error in library(FSA) : there is no package called 'FSA'
Execution halted
Packages required but not available: 'devtools', 'gh', '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:
  'ggplot2', 'rvest', 'testthat'
Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'rcrossref'
Packages required but not available: 'tibble', 'cli'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'Introduction-to-RcppHungarian.Rmd' using rmarkdown
Quitting from lines 45-57 (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
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RcppParallel/RcppParallel.Rcheck/00install.out' for details.
Running 'test-all.R'
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
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RcppUUID/RcppUUID.Rcheck/00install.out' for details.
Packages required but not available:
  'dplyr', 'forecast', 'ggmap', 'leaflet', 'leafsync'

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: 'roxygen2', 'testthat'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'Mercator'
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'czso', 'ggplot2', 'rvest', 'testthat', 'roxygen2', 'devtools',
  'dplyr', 'lwgeom'

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

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

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.
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.
Running 'run-testthat-rDEA.R'
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 required but not available: 'redland', 'readr', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'tibble', 'repurrrsive', 'nycflights13'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > 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 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
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of 'unsigned int[1]' [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of 'unsigned int[1]' [-Warray-bounds]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RDieHarder/RDieHarder.Rcheck/00install.out' for details.
Running examples in 'rdi-Ex.R' failed
The error most likely occurred in:

> ### Name: convertRDI
> ### Title: Convert RDI measures
> ### Aliases: convertRDI
> 
> ### ** Examples
> 
> 
> #create genes
> genes = sample(letters, 10000, replace=TRUE)
> #create sequence annotations
> seqAnnot = data.frame(donor = sample(1:4, 10000, replace=TRUE))
> #calculate RDI
> d = rdi(genes, seqAnnot)
> 
> ##convert RDI to actual 'lfc' estimates and compare
> dtrue = convertRDI(d)$pred
> plot(d, dtrue)
> 
> ##look at SD ranges around lfc estimates
> dtrue = convertRDI(d, calcSD=TRUE)
> 
> ##plot using ggplot2
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: 'testthat', 'vcfR'
Package required but not available: 'readxl'

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

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

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

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: 'aws.alexa', 'devtools'

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

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

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

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'leaflet', 'testthat', 'roxygen2', 'devtools', 'OSMscale', 'readr'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/re2/re2.Rcheck/00install.out' for details.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'webshot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'leaflet', 'testthat'
Packages required but not available: 'readxl', 'dplyr', 'tidyr', 'rvest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'read.gt3x-Ex.R' failed
The error most likely occurred in:

> ### 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)
> ## 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
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.
Packages required but not available: 'cellranger', 'readr'

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: 'readxl', 'tidyr', 'dplyr', 'rvest'

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: 'cli', 'tibble', 'vroom'

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:
  'readODS', 'readxl', 'streamR', 'tibble'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cellranger', '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:
  'ggplot2', 'plotly', 'testthat', 'tidyr', 'xpectr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'recexcavAAR-vignette-1.Rmd' using rmarkdown
Quitting from lines 27-33 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'recexcavAAR-vignette-1.Rmd'

--- re-building 'recexcavAAR-vignette-2.Rmd' using rmarkdown
Quitting from lines 25-29 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'recexcavAAR-vignette-2.Rmd'

--- re-building 'recexcavAAR-vignette-3.Rmd' using rmarkdown
Loading required package: kriging
Transformation: 
 local centroid: 3.66666666666667 2.66666666666667 
 absolute centroid: 578172.831 6017856.63333333 
 scale: 1.08105445197455 
 rotation arc: 216.864428620413
--- finished re-building 'recexcavAAR-vignette-3.Rmd'

SUMMARY: processing the following files failed:
  'recexcavAAR-vignette-1.Rmd' 'recexcavAAR-vignette-2.Rmd'

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

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'Evaluating_recommender_systems.Rmd' using rmarkdown
'MatrixExtra' modifies important behaviors from 'Matrix'. See ?MatrixExtra-options.
Quitting from lines 281-300 (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
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 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 suggested but not available for checking:
  'testthat', 'prevR', 'fields'
Running examples in 'recurse-Ex.R' failed
The error most likely occurred in:

> ### Name: drawCircle
> ### Title: Draws a circle
> ### Aliases: drawCircle
> 
> ### ** Examples
> 
> data(martin)
> revisits = getRecursions(martin, radius = 1)
> plot(revisits, martin, legendPos = c(10, -15))
Error: fields package needed for legend. Please install it.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'recurse.Rmd' using rmarkdown
Loading required package: recurse
Loading required package: scales
Loading required package: sp
Quitting from lines 57-65 (recurse.Rmd) 
Error: processing vignette 'recurse.Rmd' failed with diagnostics:
fields package needed for legend. Please install it.
--- failed re-building 'recurse.Rmd'

SUMMARY: processing the following file failed:
  'recurse.Rmd'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'car', 'UsingR'
Packages required but not available: 'readr', 'tidyr'

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

> ### Name: build_r_data_package
> ### Title: Build R Data Package
> ### Aliases: build_r_data_package build_r_data_package.rcer_rccore
> ###   build_r_data_package.default
> 
> ### ** Examples
> 
> ## Please read the vignette for examples:
> ## vignette(topic = "export", package = "REDCapExporter")
> 
> library(REDCapExporter)
> # avs_raw_core <- export_core()
> data(avs_raw_core)
> tmppth <- tempdir()
> build_r_data_package(avs_raw_core, tmppth, author_roles = list(dewittp = c("cre", "aut")))
Warning in format_record.rcer_raw_record(x$record_raw, x$metadata_raw) :
  At least one of the columns is an S4 class.
  data.table might not work correctly for
  atoi, atoi_postseason
  check status of https://github.com/Rdatatable/data.table/issues/4315
  and https://github.com/dewittpe/REDCapExporter/issues/17
Creating source package at C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\REDCapExporter\tmp\RtmpGUBwfC\rcd14465
Error in loadNamespace(x) : there is no package called 'devtools'
Calls: build_r_data_package ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'api.Rmd' using rmarkdown
Quitting from lines 53-62 (api.Rmd) 
Error: processing vignette 'api.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building 'api.Rmd'

--- re-building 'export.Rmd' using rmarkdown
Quitting from lines 29-33 (export.Rmd) 
Error: processing vignette 'export.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building 'export.Rmd'

SUMMARY: processing the following files failed:
  'api.Rmd' 'export.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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 suggested but not available for checking:
  'dplyr', 'kableExtra', 'TCGAbiolinks', 'qvalue'
Error(s) in re-building vignettes:
--- re-building 'Rediscover.Rmd' using rmarkdown
Loading required package: Matrix
Loading required package: speedglm
Loading required package: MASS
Loading required package: PoissonBinomial
Quitting from lines 21-30 (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:
  'dplyr', 'sf', 'ggplot2', 'patchwork', 'readr'

Packages suggested but not available for checking:
  'lwgeom', 'rmapshaper', 'spdep', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'REEMtree-Ex.R' failed
The error most likely occurred in:

> ### 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
Package required but not available: 'spdep'

Package suggested but not available for checking: 'rcrossref'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'refinr-vignette.Rmd' using rmarkdown
Quitting from lines 84-116 (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.
Packages required but not available: 'golem', 'tidyr', 'pkgload', 'rvest'

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'geepack', 'mice', 'modelr', 'testthat', 'tidyverse'
Namespace in Imports field not imported from: 'Deriv'
  All declared Imports should be used.
Packages required but not available:
  'ggplot2', 'dplyr', 'forcats', 'rattle'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'GA', 'caret', 'semPlot'
Error(s) in re-building vignettes:
--- re-building 'short_intro.Rmd' using knitr
Quitting from lines 45-46 (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.
Packages required but not available: 'ggplot2', 'mice'

Package suggested but not available for checking: 'testthat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'restrictions.Rmd' using rmarkdown
Quitting from lines 73-96 (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
Packages required but not available:
  'readxl', 'ggforce', 'ggplot2', 'dplyr', 'sf'

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'gWidgets2tcltk'
  All declared Imports should be used.
Package required but not available: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'mockery', 'pkgbuild', 'testthat'
Packages suggested but not available for checking: 'statnet', 'ggplot2'
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.
Error(s) in re-building vignettes:
--- re-building 'rentrez_tutorial.Rmd' using rmarkdown
Quitting from lines 15-28 (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:
  'cli', 'devtools', 'testthat'
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.
Packages required but not available: 'blavaan', 'mice'

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

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

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

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

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:
  'brms', 'dplyr', 'ivreg', 'rstanarm', 'testthat'
Package suggested but not available for checking: 'tourr'
Running examples in 'REPPlab-Ex.R' failed
The error most likely occurred in:

> ### Name: EPPlab
> ### Title: Function for Exploratory Projection Pursuit.
> ### Aliases: EPPlab
> 
> ### ** Examples
> 
> 
>   library(tourr)
Error in library(tourr) : there is no package called 'tourr'
Execution halted
Package required but not available: 'cli'

Packages suggested but not available for checking:
  'sessioninfo', 'styler', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', '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:
  'googledrive', 'qs', 'sf', 'testthat'
Packages unavailable to check Rd xrefs: 'googledrive', 'sf'
Error(s) in re-building vignettes:
--- re-building 'Cache-using-postgresql.Rmd' using rmarkdown
--- finished re-building 'Cache-using-postgresql.Rmd'

--- re-building 'Intro-to-Cache.Rmd' using rmarkdown
Failed with error:  'there is no package called 'googledrive''
Quitting from lines 105-116 (Intro-to-Cache.Rmd) 
Error: processing vignette 'Intro-to-Cache.Rmd' failed with diagnostics:
googledrive is required but not yet installed. Try: install.packages('googledrive') to use google drive files
--- failed re-building 'Intro-to-Cache.Rmd'

SUMMARY: processing the following file failed:
  'Intro-to-Cache.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'pillar'

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

Packages which this enhances but not available for checking:
  'tibble', 'plotly', 'geojsonio'

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

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

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

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'parsedate', 'plotdap', 'readr', 'rerddap', 'sf'

Package suggested but not available for checking: 'gganimate'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'haven', 'readr', 'readxl', 'dplyr', 'dbplyr',
  'RMariaDB', 'sparklyr'
Packages required but not available: 'PKNCA', 'marelac', 'seacarb'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'lintr'
Namespace in Imports field not imported from: 'Rserve'
  All declared Imports should be used.
Packages required but not available: 'useful', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'RTriangle'
  All declared Imports should be used.
Package required but not available: 'textreadr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'Intro_To_retrodesign.Rmd' using rmarkdown
Quitting from lines 20-24 (Intro_To_retrodesign.Rmd) 
Error: processing vignette 'Intro_To_retrodesign.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Intro_To_retrodesign.Rmd'

SUMMARY: processing the following file failed:
  'Intro_To_retrodesign.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'DT'
  All declared Imports should be used.
Packages required but not available:
  'bigrquery', 'dbplyr', 'dplyr', 'gargle', 'golem', 'pkgload',
  'redcapAPI', 'REDCapR', 'tibble', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.r'
Running the tests in 'tests/test-all.r' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package unavailable to check Rd xrefs: 'btergm'
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2', 'Hmisc', 'rvest', 'roxygen2'
Error(s) in re-building vignettes:
--- re-building 'log_parsing.Rmd' using rmarkdown
Quitting from lines 29-34 (log_parsing.Rmd) 
Error: processing vignette 'log_parsing.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'log_parsing.Rmd'

--- re-building 'url_parsing.Rmd' using rmarkdown
--- finished re-building 'url_parsing.Rmd'

SUMMARY: processing the following file failed:
  'log_parsing.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'cli', 'dplyr', 'pkgbuild', 'pkgload', 'tibble'

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

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.
Package required but not available: 'CCA'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'iCluster'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'dtplyr', 'tidyr', 'sf', 'ggplot2'

Package suggested but not available for checking: 'gganimate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #context("Coverage")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'readr', 'gh', '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: 'cli', 'tidyr'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'rflexscan-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.rflexscan
> ### Title: Graph plotting of flexscan results
> ### Aliases: plot.rflexscan
> 
> ### ** Examples
> 
> # load sample data (North Carolina SIDS data)
> library(spdep)
Error in library(spdep) : there is no package called 'spdep'
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'tibble', 'tidyr'

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

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

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

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

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

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'vignette_RGCCA.Rmd' using rmarkdown
Quitting from lines 87-88 (vignette_RGCCA.Rmd) 
Error: processing vignette 'vignette_RGCCA.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'vignette_RGCCA.Rmd'

SUMMARY: processing the following file failed:
  'vignette_RGCCA.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'mixOmics'

Package suggested but not available for checking: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'CRS_projections_transformations.Rmd' using rmarkdown
Quitting from lines 330-331 (CRS_projections_transformations.Rmd) 
Error: processing vignette 'CRS_projections_transformations.Rmd' failed with diagnostics:
failure in points 1
--- failed re-building 'CRS_projections_transformations.Rmd'

--- re-building 'PROJ6_GDAL3.Rmd' using rmarkdown
Quitting from lines 906-910 (PROJ6_GDAL3.Rmd) 
Error: processing vignette 'PROJ6_GDAL3.Rmd' failed with diagnostics:
failure in Polygons 1 Polygon 1 points 1
--- failed re-building 'PROJ6_GDAL3.Rmd'

--- re-building 'OGR_shape_encoding.Rnw' using Sweave
Read 1 item
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'OGR_shape_encoding.Rnw'

SUMMARY: processing the following files failed:
  'CRS_projections_transformations.Rmd' 'PROJ6_GDAL3.Rmd'

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

Packages suggested but not available for checking:
  'leaflet', 'leafsync', 'lidR', 'viridis'

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

Packages suggested but not available for checking:
  'leaflet.extras2', 'geojsonio', 'sf', 'stars', 'googledrive',
  'googleCloudStorageR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'leaflet', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'precipitation_stochastic_generation_v7.Rmd' using rmarkdown
Loading required package: copula
Loading required package: RGENERATE
Loading required package: RMAWGEN
Loading required package: chron
Loading required package: date
Loading required package: vars
Loading required package: MASS
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: urca
Loading required package: lmtest

Attaching package: 'vars'

The following object is masked from 'package:copula':

    A

Loading required package: blockmatrix
Loading required package: Matrix
Loading required package: stringr

Attaching package: 'stringr'

The following object is masked from 'package:strucchange':

    boundary


Attaching package: 'lubridate'

The following objects are masked from 'package:chron':

    days, hours, minutes, seconds, years

The following object is masked from 'package:copula':

    interval

The following objects are masked from 'package:base':

    date, intersect, setdiff, union

Quitting from lines 50-63 (precipitation_stochastic_generation_v7.Rmd) 
Error: processing vignette 'precipitation_stochastic_generation_v7.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building 'precipitation_stochastic_generation_v7.Rmd'

SUMMARY: processing the following file failed:
  'precipitation_stochastic_generation_v7.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'tests.R'
  Comparing 'tests.Rout' to 'tests.Rout.save' ... OK
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/rgeolocate/rgeolocate.Rcheck/00install.out' for details.
Packages required but not available: 'readr', 'sf'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'leafsync'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'leak_by_exception.R'
  Comparing 'leak_by_exception.Rout' to 'leak_by_exception.Rout.save' ...9a10
> g1 is invalid
11a13,17
> In addition: Warning messages:
> 1: In RGEOSUnaryPredFunc(spgeom, byid, "rgeos_isvalid") :
>   Self-intersection at or near point 5 5
> 2: In gUnion(g1, g2) :
>   Invalid objects found; consider using set_RGEOS_CheckValidity(2L)
12a19
> g1 is invalid
14a22,26
> In addition: Warning messages:
> 1: In RGEOSUnaryPredFunc(spgeom, byid, "rgeos_isvalid") :
>   Self-intersection at or near point 5 5
> 2: In gDifference(g1, g2) :
>   Invalid objects found; consider using set_RGEOS_CheckValidity(2L)
15a28
> g1 is invalid
17a31,35
> In addition: Warning messages:
> 1: In RGEOSUnaryPredFunc(spgeom, byid, "rgeos_isvalid") :
>   Self-intersection at or near point 5 5
> 2: In gIntersection(g1, g2) :
>   Invalid objects found; consider using set_RGEOS_CheckValidity(2L)
18a37
> g1 is invalid
20a40,44
> In addition: Warning messages:
> 1: In RGEOSUnaryPredFunc(spgeom, byid, "rgeos_isvalid") :
>   Self-intersection at or near point 5 5
> 2: In gSymdifference(g1, g2) :
>   Invalid objects found; consider using set_RGEOS_CheckValidity(2L)
30,31d53
< Error in TopologyFunc(spgeom, id, byid, "rgeos_pointonsurface") : 
<   TopologyException: Input geom 1 is invalid: Self-intersection at or near point 5 5 at 5 5
  Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'readr', '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:
  'sf', 'tmap', 'fields', 'rvest', 'mapview', 'stars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'webshot2', 'pkgdown', 'testthat'

Package which this enhances but not available for checking: 'waldo'
Packages required but not available:
  'gargle', 'dplyr', 'tidyr', 'cli', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'loa', 'leaflet'
Packages required but not available: 'cli', 'ckanr', '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: 'sf', 'stars'
Packages suggested but not available for checking: 'DBItest', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #
  > # This is for local testing only and should not be included when uploading to CRAN.
  > #
  > # groovyJars <- list (
  > #     "C:/.../groovy-2.4.5-indy.jar"
  > # )
  > #
  > # options(GROOVY_JARS=groovyJars)
  > #
  > 
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #'////////////////////////////////////////////////////////////////////////////
  > #' FILE: testthat.R
  > #' AUTHOR: David Ruvolo
  > #' CREATED: 2020-09-06
  > #' MODIFIED: 2020-09-06
  > #' PURPOSE: main unit testing file
  > #' STATUS: working
  > #' PACKAGES: userthis; rheroicons
  > #' COMMENTS: NA
  > #'////////////////////////////////////////////////////////////////////////////
  > 
  > # pkgs
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'patchwork'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## -*- mode: R -*-
  > ##
  > ## Copyright (C) 2019 Takeshi Abe <tabe@fixedpoint.jp>
  > ##
  > ## This program is free software: you can redistribute it and/or modify
  > ## it under the terms of the GNU General Public License as published by
  > ## the Free Software Foundation, either version 3 of the License, or
  > ## (at your option) any later version.
  > ##
  > ## This program is distributed in the hope that it will be useful,
  > ## but WITHOUT ANY WARRANTY; without even the implied warranty of
  > ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > ## GNU General Public License for more details.
  > ##
  > ## You should have received a copy of the GNU General Public License
  > ## along with this program.  If not, see <https://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'quadratic_phase_coupling.Rmd' using rmarkdown
Quitting from lines 104-118 (quadratic_phase_coupling.Rmd) 
Error: processing vignette 'quadratic_phase_coupling.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'quadratic_phase_coupling.Rmd'

SUMMARY: processing the following file failed:
  'quadratic_phase_coupling.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  RhpcMPI.c:112:28: warning: ' "' directive output may be truncated writing 2 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
  fakemaster.c:123:83: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size 4046 [-Wformat-truncation=]
  fakemaster.c:109:60: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size 4069 [-Wformat-truncation=]
  fakemaster.c:97:68: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size 4061 [-Wformat-truncation=]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Rhpc/Rhpc.Rcheck/00install.out' for details.
Package required but not available: 'lomb'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'parsedate', 'pillar', 'rcmdcheck', '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: 'riceidconverter'

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

Packages suggested but not available for checking:
  'testthat', 'pkgload', 'mimic.demo', 'eicu.demo', 'ggplot2',
  'forestmodel', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'T4cluster', 'ggrepel'

Package suggested but not available for checking: 'ggplot2'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  RInside.cpp:169:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 260 equals destination size [-Wstringop-truncation]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RInside/RInside.Rcheck/00install.out' for details.
Found the following sources/headers with CR or CRLF line endings:
  src/RInsideAutoloads.h
  src/RInsideEnvVars.h
Some Unix compilers require LF line endings.
Packages required but not available: 'haven', 'readxl', 'tibble'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'iptools', '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: 'IsingSampler'
Package required but not available: 'mlogit'

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

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

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:
  'ggplot2', 'portfolioBacktest', 'testthat'
Running examples in 'riskParityPortfolio-Ex.R' failed
The error most likely occurred in:

> ### Name: barplotPortfolioRisk
> ### Title: Create portfolio barplots with the capital allocation and the
> ###   risk allocation
> ### Aliases: barplotPortfolioRisk
> 
> ### ** Examples
> 
> library(riskParityPortfolio)
> 
> # generate random covariance matrix
> set.seed(42)
> N <- 10
> V <- matrix(rnorm(N^2), nrow = N)
> Sigma <- cov(V)
> 
> # generate random portfolio vectors
> w_single <- runif(N)
> w_single <- w_single/sum(w_single)  # normalize
> names(w_single) <- LETTERS[1:N]
> 
> w_multiple <- matrix(runif(4*N), ncol = 4)
> w_multiple <- sweep(w_multiple,  # normalize each column
+                     MARGIN = 2, 
+                     STATS = colSums(w_multiple), FUN = "/")
> rownames(w_multiple) <- LETTERS[1:N]
> 
> # plot
> barplotPortfolioRisk(w_single, Sigma)
Error: Please install package "ggplot2" or choose another plot type
Execution halted
Packages required but not available: 'ggplot2', 'rms'

Packages suggested but not available for checking:
  'casebase', 'ipw', 'flexsurv', 'mstate', 'pec', 'randomForestSRC',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'httr'
  All declared Imports should be used.
Packages required but not available: 'solrium', '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: 'imputeTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'publication-reproduction.Rmd' using rmarkdown
--- finished re-building 'publication-reproduction.Rmd'

--- re-building 'quickstart.Rmd' using rmarkdown
Loading required package: rivr
M1 profile specified. Computing upstream profile
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Quitting from lines 100-104 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building 'quickstart.Rmd'

--- re-building 'technical-vignette.Rmd' using rmarkdown
--- finished re-building 'technical-vignette.Rmd'

SUMMARY: processing the following file failed:
  'quickstart.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files for x64 is not available
File 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/rJava/rJava.Rcheck/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package required but not available: 'kableExtra'

Package suggested but not available for checking: 'ggdemetra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'XLConnect'
  All declared Imports should be used.
Package suggested but not available for checking: 'IRdisplay'
Namespaces in Imports field not imported from:
  'Matrix' 'arules' 'pmml' 'rJava'
  All declared Imports should be used.
Packages required but not available: 'tibble', 'dplyr', 'tidyr'

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

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

Package suggested but not available for checking: 'viridis'

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

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:
  'cli', 'pak', 'pillar', 'testthat'
Found the following significant warnings:
  internal/hash.c:142:16: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/rlang/rlang.Rcheck/00install.out' for details.
Running 'sink.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Workaround for loadNamespace() failure on R 3.2
  > requireNamespace("rlang")
  Loading required namespace: rlang
  > 
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'ggplot2', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Created by: Jonas Vaclavek
  > # Modified by: Jonas Vaclavek
  > # Modify date: 23.5.2019
  > # Description: Testthat config file
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'sf'

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:
  'rstantools', 'forecast', 'rstan', 'StanHeaders'

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

Packages suggested but not available for checking:
  'Seurat', 'testthat', 'fgsea'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'lmerTest'
Package required but not available: 'Luminescence'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #! /usr/bin/env Rscript
  > 
  > 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:
  'Seurat', 'readr', 'viridis', 'phateR'

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

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', 'geojsonio', 'tidyr', 'sf'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RMariaDB/RMariaDB.Rcheck/00install.out' for details.
Packages required but not available: 'tibble', 'ggplot2', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testrmd.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'ktaucenters'

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', 'merTools'
Running examples in 'rmcorr-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.rmc
> ### Title: Plot the repeated measures correlation coefficient.
> ### Aliases: plot.rmc
> 
> ### ** Examples
> 
> ## Bland Altman 1995 data
> my.rmc <- rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH, dataset = bland1995)
Warning in rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH,  :
  'Subject' coerced into a factor
> plot(my.rmc, overall = TRUE)
> 
> #using ggplot instead
> ggplot2::ggplot(bland1995, ggplot2::aes(x = PacO2, y = pH, group = factor(Subject),
+       color = factor(Subject))) +
+       ggplot2::geom_point(ggplot2::aes(colour = factor(Subject))) +
+       ggplot2::geom_line(ggplot2::aes(y = my.rmc$model$fitted.values), linetype = 1) 
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'New_rmcorr_paper_analyses_figures.Rmd' using rmarkdown
Warning in rmcorr(participant = Participant, measure1 = Age, measure2 = Volume,  :
  'Participant' coerced into a factor
Quitting from lines 595-649 (New_rmcorr_paper_analyses_figures.Rmd) 
Error: processing vignette 'New_rmcorr_paper_analyses_figures.Rmd' failed with diagnostics:
could not find function "predictInterval"
--- failed re-building 'New_rmcorr_paper_analyses_figures.Rmd'

SUMMARY: processing the following file failed:
  'New_rmcorr_paper_analyses_figures.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'rstan', 'rstantools', 'RcppParallel', 'dplyr', 'tibble', 'tidyr',
  'StanHeaders'

Package suggested but not available for checking: 'testthat'

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

--- re-building 'wordcount.Rmd' using rmarkdown
Quitting from lines 22-25 (wordcount.Rmd) 
Error: processing vignette 'wordcount.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'wordcount.Rmd'

SUMMARY: processing the following file failed:
  'wordcount.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'questionr', 'ggplot2'
Running examples in 'rmdformats-Ex.R' failed
The error most likely occurred in:

> ### Name: pilltabs
> ### Title: Given a cross-table, outputs HTML code to display several views
> ###   of with a tabbed interface
> ### Aliases: pilltabs
> 
> ### ** Examples
> 
> 
> data(airquality)
> tab <- table(airquality$Month, airquality$Ozone > 25)
> pilltabs(tab)
Error: the questionr package is needed for the pilltabs() function to work. Please install it.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'pkgdown', 'dplyr', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'rmdpartials.Rmd' using rmarkdown
Quitting from lines 26-32 (rmdpartials.Rmd) 
Error: processing vignette 'rmdpartials.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'rmdpartials.Rmd'

SUMMARY: processing the following file failed:
  'rmdpartials.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'adabag'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'Rmisc-Ex.R' failed
The error most likely occurred in:

> ### Name: group.CI
> ### Title: Group Confidence Interval
> ### Aliases: group.CI
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> require(latticeExtra)
Loading required package: latticeExtra
> with(group.CI(weight~feed,chickwts),
+  segplot(feed~weight.lower+weight.upper,center=weight.mean)
+ )
> 
> require(Hmisc)
Loading required package: Hmisc
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Hmisc'
> with(group.CI(Temp~Month,airquality),
+  xYplot(Cbind(Temp.mean,Temp.lower,Temp.upper)~numericScale(Month),type="b",ylim=c(60,90))
+ )
Error in xYplot(Cbind(Temp.mean, Temp.lower, Temp.upper) ~ numericScale(Month),  : 
  could not find function "xYplot"
Calls: with -> with.default -> eval -> eval
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # MixtComp version 4.0  - july 2019
  > # Copyright (C) Inria - Université de Lille - CNRS
  > 
  > # This program is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU Affero General Public License as
  > # published by the Free Software Foundation, either version 3 of the
  > # License, or (at your option) any later version.
  > # This program is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU Affero General Public License for more details.
  > # 
  > # You should have received a copy of the GNU Affero General Public License
  > # along with this program.  If not, see <https://www.gnu.org/licenses/>
  >  
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'RMixtCompUtilities', 'ggplot2', 'plotly'

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

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

--- re-building 'gff-processing.Rmd' using rmarkdown
Quitting from lines 102-131 (gff-processing.Rmd) 
Error: processing vignette 'gff-processing.Rmd' failed with diagnostics:
there is no package called 'readr'
--- failed re-building 'gff-processing.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'nozzle.Rmd' using rmarkdown
--- finished re-building 'nozzle.Rmd'

SUMMARY: processing the following file failed:
  'gff-processing.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ecr', 'ggplot2', 'dplyr', '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: 'pkgbuild'
Packages required but not available:
  'rms', 'RcppParallel', 'rstan', 'rstantools', 'Hmisc', 'ggplot2',
  'StanHeaders'

Package suggested but not available for checking: 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'dplyr', 'tbl2xts'

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

Packages suggested but not available for checking: 'plotly', 'mice', 'rmsb'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following sources/headers with CR or CRLF line endings:
  src/lib/scotch_6.0.9/include/scotch.h
  src/lib/scotch_6.0.9/include/scotchf.h
  src/lib/scotch_6.0.9/src/libscotch/scotch.h
  src/lib/scotch_6.0.9/src/libscotch/scotchf.h
Some Unix compilers require LF line endings.
Packages required but not available:
  'dplyr', 'ggplot2', 'pdp', 'tibble', 'viridis'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'RMariaDB', 'testthat'
Packages required but not available: 'ggplot2', 'hot.deck'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'httptest', 'testthat', 'ggplot2'
Packages required but not available: 'gaston', 'RcppParallel'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

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:
  'rdflib', 'rfigshare', 'testthat', 'taxadb'

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

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

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

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

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

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

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

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

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

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: 'beadarray'

Package suggested but not available for checking: 'beadarrayExampleData'

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

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'future'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'using_robotstxt.Rmd' using rmarkdown

 google.com                      


 google.com                      

Quitting from lines 63-65 (using_robotstxt.Rmd) 
Error: processing vignette 'using_robotstxt.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'using_robotstxt.Rmd'

SUMMARY: processing the following file failed:
  'using_robotstxt.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'GSE'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'gapminder', 'readr', 'dplyr', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'gallery.Rmd' using rmarkdown
Quitting from lines 72-87 (gallery.Rmd) 
Error: processing vignette 'gallery.Rmd' failed with diagnostics:
there is no package called 'readr'
--- failed re-building 'gallery.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 169-189 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'gapminder'
--- failed re-building 'introduction.Rmd'

--- re-building 'shiny.Rmd' using rmarkdown
--- finished re-building 'shiny.Rmd'

SUMMARY: processing the following files failed:
  'gallery.Rmd' 'introduction.Rmd'

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

Package which this enhances but not available for checking: 'Hmisc'
Errors in running code in vignettes:
when running code in 'lmrob_simulation.Rnw'

> options(width = 60, warn = 1)

> if (FALSE) {
+     options(cores = max(1, parallel::detectCores() - 2))
+ } else {
+     options(cores = min(2, parallel::detectCores()))
+ }

> N <- 1000

> robustDoc <- system.file("doc", package = "robustbase")

> robustDta <- robustDoc

> source(file.path(robustDoc, "simulation.init.R"))
Loading required package: xtable
Loading required package: robustbase

> trim <- 0.1

> stopifnot(require(ggplot2), require(GGally), require(grid), 
+     require(reshape2))
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'

  When sourcing 'lmrob_simulation.R':
Error: require(ggplot2) is not TRUE
Execution halted

  'fastMcd-kmini.Rnw' using 'UTF-8'... OK
  'lmrob_simulation.Rnw' using 'UTF-8'... failed
  'psi_functions.Rnw' using 'UTF-8'... OK
Error(s) in re-building vignettes:
--- re-building 'fastMcd-kmini.Rnw' using Sweave
Loading required package: robustbase
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'fastMcd-kmini.Rnw'

--- re-building 'lmrob_simulation.Rnw' using Sweave
Loading required package: xtable
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'

Error: processing vignette 'lmrob_simulation.Rnw' failed with diagnostics:
 chunk 2 (label = graphics-setup) 
Error : require(ggplot2) is not TRUE

--- failed re-building 'lmrob_simulation.Rnw'

--- re-building 'psi_functions.Rnw' using Sweave
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'psi_functions.Rnw'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'Hmisc', 'car'
Package unavailable to check Rd xrefs: 'HH'
Packages required but not available: 'dplyr', 'DiagrammeR', 'ggplot2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'progress'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'tidyr', 'tibble', '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: 'DiagrammeR', 'ggplot2', 'flexsurv'

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

Attaching package: 'rODE'

The following object is masked from 'package:stats':

    step

--- finished re-building 'Comparison.Rmd'

--- re-building 'ErrorEuler.Rmd' using rmarkdown
Quitting from lines 27-65 (ErrorEuler.Rmd) 
Error: processing vignette 'ErrorEuler.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ErrorEuler.Rmd'

--- re-building 'FallingParticle.Rmd' using rmarkdown
Quitting from lines 103-147 (FallingParticle.Rmd) 
Error: processing vignette 'FallingParticle.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'FallingParticle.Rmd'

--- re-building 'Kepler.Rmd' using rmarkdown
--- finished re-building 'Kepler.Rmd'

--- re-building 'Muskat-MBal.Rmd' using rmarkdown
Quitting from lines 51-89 (Muskat-MBal.Rmd) 
Error: processing vignette 'Muskat-MBal.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Muskat-MBal.Rmd'

--- re-building 'Pendulum.Rmd' using rmarkdown
Quitting from lines 87-132 (Pendulum.Rmd) 
Error: processing vignette 'Pendulum.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Pendulum.Rmd'

--- re-building 'Planet.Rmd' using rmarkdown
--- finished re-building 'Planet.Rmd'

--- re-building 'Projectile.Rmd' using rmarkdown
Quitting from lines 16-88 (Projectile.Rmd) 
Error: processing vignette 'Projectile.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Projectile.Rmd'

--- re-building 'Reaction.Rmd' using rmarkdown
--- finished re-building 'Reaction.Rmd'

SUMMARY: processing the following files failed:
  'ErrorEuler.Rmd' 'FallingParticle.Rmd' 'Muskat-MBal.Rmd'
  'Pendulum.Rmd' 'Projectile.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'verification'
Packages suggested but not available for checking:
  'testthat', 'roll', 'RcppParallel'
Error(s) in re-building vignettes:
--- re-building 'Comparisons.Rmd' using rmarkdown

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Quitting from lines 28-71 (Comparisons.Rmd) 
Error: processing vignette 'Comparisons.Rmd' failed with diagnostics:
there is no package called 'roll'
--- failed re-building 'Comparisons.Rmd'

SUMMARY: processing the following file failed:
  'Comparisons.Rmd'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'someFIGIs.R'
Running the tests in 'tests/someFIGIs.R' failed.
Complete output:
  > library(ROpenFIGI)
  > jsondf <- data.frame(idType=c("ID_ISIN"),idValue=c("US922646AS37"),
  +                      exchCode=c(NA),currency=NA,micCode=NA,stringsAsFactors = F)
  > 
  > jsonrst <- OpenFIGI(jsondf)
  > jsonrst
  [[1]]
            figi                  name             ticker exchCode compositeFIGI
  1 BBG00004SPH6 REPUBLIC OF VENEZUELA VENZ 9.25 09/15/27  EUROTLX            NA
    uniqueID securityType marketSector shareClassFIGI uniqueIDFutOpt
  1       NA       GLOBAL         Govt             NA             NA
    securityType2 securityDescription
  1          Govt VENZ 9 1/4 09/15/27
  
  > 
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Packages required but not available:
  'dplyr', 'haven', 'readr', 'rio', 'tibble', 'tidyr'

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', 'rcrossref'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'ggplot2', 'ggrepel', 'rio', 'ufs', 'kableExtra', 'viridis'

Packages suggested but not available for checking:
  'GGally', 'MBESS', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'cartography', 'testthat'
Packages required but not available: 'mrfDepth', 'rrcovHD'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'fulltext', 'phylobase', 'readxl', 'RNeXML', 'testthat'
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > ###
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'data_mashups.Rmd' using rmarkdown
Quitting from lines 151-155 (data_mashups.Rmd) 
Error: processing vignette 'data_mashups.Rmd' failed with diagnostics:
there is no package called 'phylobase'
--- failed re-building 'data_mashups.Rmd'

--- re-building 'meta-analysis.Rmd' using rmarkdown
--- finished re-building 'meta-analysis.Rmd'

--- re-building 'rotl.Rmd' using rmarkdown
--- finished re-building 'rotl.Rmd'

SUMMARY: processing the following file failed:
  'data_mashups.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'httpuv' 'utils'
  All declared Imports should be used.
Packages required but not available: 'devtools', 'tibble', 'usethis'

Package suggested but not available for checking: 'testthat'

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

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: 'bipartite', 'fields'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'rpdo-Ex.R' failed
The error most likely occurred in:

> ### Name: pdo
> ### Title: Pacific Decadal Oscillation Index
> ### Aliases: pdo
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(rpdo)
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: 'testthat', 'RobStatTM'
Running examples in 'RPEIF-Ex.R' failed
The error most likely occurred in:

> ### Name: IF.robMean
> ### Title: Influence Function - Robust M-Estimator of Mean
> ### Aliases: IF.robMean
> 
> ### ** Examples
> 
> data(edhec, package = "PerformanceAnalytics")
> colnames(edhec) = c("CA", "CTAG", "DIS", "EM","EMN", "ED", "FIA",
+                     "GM", "LS", "MA", "RV", "SS", "FoF") 
>                     
> # Plot of IF shape
> outIF <- IF.robMean(returns = edhec[,"CA"], evalShape = TRUE, 
+                     retVals = NULL, 
+                     IFplot = TRUE, IFprint = TRUE)
Error in loadNamespace(x) : there is no package called 'RobStatTM'
Calls: IF.robMean ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'RobStatTM'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'customitem.Rmd' using knitr
Loading required package: parallel
RPF is not compiled to take advantage of computers with multiple cores.
--- finished re-building 'customitem.Rmd'

--- re-building 'diagnostics.Rmd' using knitr
Quitting from lines 7-13 (diagnostics.Rmd) 
Error: processing vignette 'diagnostics.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'diagnostics.Rmd'

--- re-building 'flexmirt-plots.Rmd' using knitr
Quitting from lines 7-13 (flexmirt-plots.Rmd) 
Error: processing vignette 'flexmirt-plots.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'flexmirt-plots.Rmd'

SUMMARY: processing the following files failed:
  'diagnostics.Rmd' 'flexmirt-plots.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'devtools', 'dplyr'
Error(s) in re-building vignettes:
--- re-building 'NEWS.Rmd' using rmarkdown
--- finished re-building 'NEWS.Rmd'

--- re-building 'rpivotTableIntroduction.Rmd' using rmarkdown
Quitting from lines 103-110 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'rpivotTableIntroduction.Rmd'

SUMMARY: processing the following file failed:
  'rpivotTableIntroduction.Rmd'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("rpmodel")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > #' @import testthat
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'RcppParallel', '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:
  'testthat', 'dplyr', 'dbplyr'
Packages unavailable to check Rd xrefs: 'dplyr', 'dbplyr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright (c) Facebook, Inc. and its affiliates.
  > # All rights reserved.
  > #
  > # This source code is licensed under the BSD-style license found in the
  > # LICENSE file in the root directory of this source tree.
  > 
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'flexsurv', 'flexsurvcure', 'rms', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'multiple-files.Rmd' using rmarkdown
--- finished re-building 'multiple-files.Rmd'

--- re-building 'parsing-summary.Rmd' using rmarkdown
--- finished re-building 'parsing-summary.Rmd'

--- re-building 'quick-start-demo.Rmd' using rmarkdown
Quitting from lines 141-148 (quick-start-demo.Rmd) 
Error: processing vignette 'quick-start-demo.Rmd' failed with diagnostics:
there is no package called 'readr'
--- failed re-building 'quick-start-demo.Rmd'

SUMMARY: processing the following file failed:
  'quick-start-demo.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggpubr'
Error(s) in re-building vignettes:
--- re-building 'Rpvt.Rmd' using rmarkdown
Quitting from lines 115-172 (Rpvt.Rmd) 
Error: processing vignette 'Rpvt.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Rpvt.Rmd'

SUMMARY: processing the following file failed:
  'Rpvt.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'roxygen2'
Error(s) in re-building vignettes:
--- re-building 'CoupledHarmonics.Rmd' using rmarkdown
Quitting from lines 16-19 (CoupledHarmonics.Rmd) 
Error: processing vignette 'CoupledHarmonics.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'CoupledHarmonics.Rmd'

--- re-building 'CoupledHarmonics2.Rmd' using rmarkdown
Quitting from lines 16-19 (CoupledHarmonics2.Rmd) 
Error: processing vignette 'CoupledHarmonics2.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'CoupledHarmonics2.Rmd'

--- re-building 'CoupledTwoLevelSystems.Rmd' using rmarkdown
--- finished re-building 'CoupledTwoLevelSystems.Rmd'

SUMMARY: processing the following files failed:
  'CoupledHarmonics.Rmd' 'CoupledHarmonics2.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'NatureSounds'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'Rraven.Rmd' using rmarkdown
Loading required package: tuneR
Loading required package: seewave
Loading required package: NatureSounds
Loading required package: knitr

NOTE: functions have been renamed (run 'print(new_function_names)' to see new names). Both old and new names are available in this version 
 Please see citation('warbleR') for use in publication
Quitting from lines 35-56 (Rraven.Rmd) 
Error: processing vignette 'Rraven.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'Rraven.Rmd'

SUMMARY: processing the following file failed:
  'Rraven.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'RobStatTM'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'biwavelet'
Packages suggested but not available for checking:
  'car', 'ddpcr', 'geomorph', 'kableExtra', 'ggplot2', 'evolqg'
Package unavailable to check Rd xrefs: 'evolqg'
Packages required but not available: 'dplyr', 'ggplot2', 'plotly', 'GGally'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'ragged.Rmd' using rmarkdown
Quitting from lines 49-55 (ragged.Rmd) 
Error: processing vignette 'ragged.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ragged.Rmd'

--- re-building 'rescaling_data.Rmd' using rmarkdown
Quitting from lines 50-56 (rescaling_data.Rmd) 
Error: processing vignette 'rescaling_data.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'rescaling_data.Rmd'

SUMMARY: processing the following files failed:
  'ragged.Rmd' 'rescaling_data.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'moonBook', 'editData', 'ggpubr', 'readr'

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

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: 'sf', 'stars', 'tibble'

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:
  'plotly', 'biomaRt', 'ggplot2', 'spdep', 'rworldmap'
Running examples in 'R.SamBada-Ex.R' failed
The error most likely occurred in:

> ### Name: plotManhattan
> ### Title: Manhattan plot
> ### Aliases: plotManhattan
> 
> ### ** Examples
> 
> # Example with data from the package
> # First copy needed files into the temporary directory
> file.copy(system.file("extdata", "uganda-subset-mol-Out-2.csv", package = "R.SamBada"), 
+     file.path(tempdir(),'uganda-subset-mol-Out-2.csv'), overwrite=TRUE)
[1] TRUE
> file.copy(system.file("extdata", "uganda-subset-mol-storey.csv", package = "R.SamBada"), 
+     file.path(tempdir(),'uganda-subset-mol-storey.csv'), overwrite=TRUE)
[1] TRUE
> if(Sys.info()['sysname']=='Windows'){
+   file.copy(system.file("extdata", "uganda-subset-mol_windows.gds", package = "R.SamBada"),
+       file.path(tempdir(),'uganda-subset-mol.gds'), overwrite=TRUE) #If you run Windows
+ } else {
+   file.copy(system.file("extdata", "uganda-subset-mol_unix.gds", package = "R.SamBada"),
+       file.path(tempdir(),'uganda-subset-mol.gds'), overwrite=TRUE) #If you run Unix
+ }
[1] TRUE
> # Run prepareOutput
> prep=prepareOutput(file.path(tempdir(),'uganda-subset-mol'),2,popStr=TRUE,
+      interactiveChecks=FALSE)
> ###################
> # Run plotManhattan
> ###################
> plotManhattan(prep, c('bio1'),chromo='all',valueName='pvalueG')
Error: Package "ggplot2" needed for this function to work. Please install it.
Execution halted
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if ( ! isTRUE(tryCatch({rscala::scalaConfig(reconfig="offline")}, error=function(e) TRUE)) ) {
  +   library(testthat)
  +   library(rscala)
  +   test_check("rscala")
  + }
  
  Searching the system for Java.
    Failure with rscala home directory.
    Failure with JAVACMD environment variable.
    Failure with JAVA_HOME environment variable.
    Success with PATH environment variable.
    ... querying Java specifics.
  
  Searching the system for Scala.
    Failure with rscala home directory.
    Failure with SCALACMD environment variable.
    Failure with SCALA_HOME environment variable.
    Failure with PATH environment variable.
    Success with rscala package directory.
    ... querying Scala specifics.
  
  Searching the system for SBT.
    Failure with rscala home directory.
    Failure with SBTCMD environment variable.
    Failure with SBT_HOME environment variable.
    Failure with PATH environment variable.
    Failure with rscala package directory.
    Failure with rscala temporary directory.
  
  
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following significant warnings:
  cli.c:232:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RSclient/RSclient.Rcheck/00install.out' for details.
Packages required but not available: 'tidyr', 'dplyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'tibble', 'ggplot2', 'ggpolypath', 'FactoMineR',
  'labelled'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'Rcompression'
Namespaces in Imports field not imported from:
  'binman' 'httr'
  All declared Imports should be used.
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Rserve/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for x64 is not available
File 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Rserve/Rserve.Rcheck/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Packages required but not available: 'dplyr', 'tibble'

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

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

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

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

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

Packages suggested but not available for checking:
  'aire.zmvm', 'testthat', 'ggplot2', 'ggmap', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat-build.R'
Running the tests in 'tests/testthat-build.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: 'mlxR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'NeuralNetTools'
Found the following significant warnings:
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RSNNS/RSNNS.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'readr'
Package suggested but not available for checking: 'nycflights13'
Packages required but not available: 'spatialEco', 'tigris'

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

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: 'golem', 'shinyFiles', 'disk.frame'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'DBItest', 'gh', 'rvest', 'testthat'
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'lintr', 'pkgdown'
Namespaces in Imports field not imported from:
  'RSQLite' 'knitr'
  All declared Imports should be used.
Package required but not available: 'GMMAT'

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

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

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

Package suggested but not available for checking: 'testthat'

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

Packages suggested but not available for checking:
  'shinystan', 'bayesplot', 'rstantools'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'mstate'
Packages unavailable to check Rd xrefs: 'mstate', 'flexsurv'
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rnw' using Sweave
Loading required package: survival
Loading required package: splines

Attaching package: ‘rstpm2’

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

    colon

texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building ‘Introduction.Rnw’

--- re-building ‘SimpleGuide.Rnw’ using Sweave

Error: processing vignette 'SimpleGuide.Rnw' failed with diagnostics:
 chunk 5 
Error in library(ggplot2) : there is no package called ‘ggplot2’

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

--- re-building ‘multistate.Rnw’ using Sweave
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building ‘multistate.Rnw’

--- re-building ‘predictnl.Rnw’ using Sweave
Warning in survfit.coxph(obj, se.fit = FALSE) :
  the model contains interactions; the default curve based on columm means of the X matrix is almost certainly not useful. Consider adding a newdata argument.
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building ‘predictnl.Rnw’

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

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mc2d'
  All declared Imports should be used.
Package required but not available: 'inlmisc'

Package suggested but not available for checking: 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'rsvd-Ex.R' failed
The error most likely occurred in:

> ### Name: rpca
> ### Title: Randomized principal component analysis (rpca).
> ### Aliases: rpca
> 
> ### ** Examples
> 
> 
> library('rsvd')
> #
> # Load Edgar Anderson's Iris Data
> #
> data('iris')
> 
> #
> # log transform
> #
> log.iris <- log( iris[ , 1:4] )
> iris.species <- iris[ , 5]
> 
> #
> # Perform rPCA and compute only the first two PCs
> #
> iris.rpca <- rpca(log.iris, k=2)
> summary(iris.rpca) # Summary
                         PC1   PC2
Explained variance     2.933 0.907
Standard deviations    1.712 0.952
Proportion of variance 0.733 0.227
Cumulative proportion  0.733 0.960
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952

Eigenvalues:
[1] 2.933 0.907

Rotation:
                PC1    PC2
Sepal.Length -0.504 -0.455
Sepal.Width   0.302 -0.889
Petal.Length -0.577 -0.034
Petal.Width  -0.567 -0.035
> 
> #
> # Use rPCA to compute all PCs, similar to \code{prcomp}
> #
> iris.rpca <- rpca(log.iris)
> summary(iris.rpca) # Summary
                         PC1   PC2   PC3   PC4
Explained variance     2.933 0.907 0.133 0.027
Standard deviations    1.712 0.952 0.365 0.166
Proportion of variance 0.733 0.227 0.033 0.007
Cumulative proportion  0.733 0.960 0.993 1.000
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952 0.365 0.166

Eigenvalues:
[1] 2.933 0.907 0.133 0.027

Rotation:
                PC1    PC2    PC3    PC4
Sepal.Length  0.504 -0.455  0.709  0.191
Sepal.Width  -0.302 -0.889 -0.331 -0.091
Petal.Length  0.577 -0.034 -0.219 -0.786
Petal.Width   0.567 -0.035 -0.583  0.580
> plot(iris.rpca) # Produce screeplot, variable and individuls factor maps.
Error: The package 'ggplot2' is needed for this function to work. Please install it.
Execution halted
Running examples in 'rsvg-Ex.R' failed
The error most likely occurred in:

> ### Name: rsvg
> ### Title: Render SVG into Bitmap
> ### Aliases: rsvg rsvg_raw rsvg_webp rsvg_png rsvg_pdf rsvg_svg rsvg_ps
> 
> ### ** Examples
> 
> # create some svg
> options(example.ask=FALSE)
> tmp <- tempfile()
> svglite::svglite(tmp, width = 10, height = 7)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = factor(cyl))
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2021-08-04 r80708)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 20348)

Matrix products: default

locale:
[1] LC_COLLATE=C                          
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_4.2.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Packages suggested but not available for checking:
  'dplyr', 'tibble', 'tidyr', 'testthat'
Running examples in 'rtables-Ex.R' failed
The error most likely occurred in:

> ### Name: select_all_levels
> ### Title: Add Combination Levels to split
> ### Aliases: select_all_levels add_combo_levels
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(tibble)
Error in library(tibble) : there is no package called 'tibble'
Execution halted
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'sf', 'rnaturalearth'
Error(s) in re-building vignettes:
--- re-building 'reanalysis_rr98.Rmd' using rmarkdown
Loading required package: rtdists
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'dplyr'
Loading required package: tidyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'tidyr'
Loading required package: purrr
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: binom
Quitting from lines 29-52 (reanalysis_rr98.Rmd) 
Error: processing vignette 'reanalysis_rr98.Rmd' failed with diagnostics:
could not find function "ungroup"
--- failed re-building 'reanalysis_rr98.Rmd'

SUMMARY: processing the following file failed:
  'reanalysis_rr98.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FactoMineR', 'explor', 'testthat', 'tm.plugin.factiva'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rNOMADS'
Namespace in Imports field not imported from: 'lifecycle'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RSQLite' 'stats'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'rtf.Rnw' using Sweave

Error: processing vignette 'rtf.Rnw' failed with diagnostics:
 chunk 29 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'rtf.Rnw'

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

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

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

Packages suggested but not available for checking:
  'devtools', 'sjmisc', 'sjPlot'

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

Packages suggested but not available for checking: 'Gviz', 'rtracklayer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'dplyr', 'tidyr', 'ggplot2', 'tibbletime', 'forecast',
  'tidyquant', 'readr', 'tsibble', 'feasts', 'fabletools', 'plotly',
  'timetk', 'tidyverse'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'transfer-entropy.Rmd' using rmarkdown
Quitting from lines 13-52 (transfer-entropy.Rmd) 
Error: processing vignette 'transfer-entropy.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'transfer-entropy.Rmd'

SUMMARY: processing the following file failed:
  'transfer-entropy.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'attributes.R'
  Comparing 'attributes.Rout' to 'attributes.Rout.save' ... OK
  Running 'basic.R'
  Comparing 'basic.Rout' to 'basic.Rout.save' ... OK
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'alfred'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'RStoolbox', 'moveVis', 'dplyr', 'sf', 'tidyr', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'withr'
  All declared Imports should be used.
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'plotly', 'colourpicker', 'tidyr',
  'devtools'

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

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

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

Package suggested but not available for checking: 'ggplot2'

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

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

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

Package suggested but not available for checking: 'tidymodels'

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

> ### Name: scrape
> ### Title: Softball Webscraper
> ### Aliases: scrape
> 
> ### ** Examples
> 
> url <-"https://wmubroncos.com/sports/softball/stats/2019"
> test <- scrape(url)
Error: Package "rvest" needed for this function to work. Please install it.
Execution halted
Running 'checkinputs.R'
  Running 'checkmethods.R'
  Running 'checkmodule.R'
  Running 'checkstudy.R'
  Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespace in Imports field not imported from: 'urltools'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'sessioninfo', 'cowplot'
Error(s) in re-building vignettes:
--- re-building 'using-runstats.Rmd' using rmarkdown
Quitting from lines 90-92 (using-runstats.Rmd) 
Error: processing vignette 'using-runstats.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'using-runstats.Rmd'

SUMMARY: processing the following file failed:
  'using-runstats.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'run_testthat.R'
Running the tests in 'tests/run_testthat.R' failed.
Complete output:
  > ## Load package 'testthat' 
  > if(! require("testthat", quietly=TRUE)) {
  +   message("\nCannot run unit tests -- package 'testthat' is not available!\n")
  + }
  
  Cannot run unit tests -- package 'testthat' is not available!
  
  > 
  > ## run testthat tests
  > test_check("Runuran", reporter=c("summary","check","fail"))
  Error in test_check("Runuran", reporter = c("summary", "check", "fail")) : 
    could not find function "test_check"
  Execution halted
Packages required but not available: 'testthat', 'taxize'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'bang', 'revdbayes', 'testthat'
Packages suggested but not available for checking: 'ruv', 'testthat'
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'colourpicker'

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

Package suggested but not available for checking: 'FSA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'clusterProfiler', 'dplyr', 'ggplot2', 'ggpubr', 'haven', 'msigdbr',
  'plotly', 'rWikiPathways', 'tibble', 'tidyr'

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

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

> ### Name: plot.rvine_structure
> ### Title: Plotting R-vine structures
> ### Aliases: plot.rvine_structure plot.rvine_matrix
> 
> ### ** Examples
> 
> plot(cvine_structure(1:5))
Error in plot.vinecop_dist(vinecop_dist(pcs, x), ...) : 
  The 'ggraph' package must be installed to plot.
Calls: plot -> plot.rvine_structure -> plot.vinecop_dist
Execution halted
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: 'plotly'

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

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'

Package suggested but not available for checking: 'kableExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/RWinEdt/RWinEdt.Rcheck/00install.out' for details.
Package required but not available: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rworldmap'
Packages suggested but not available for checking: 'cranly', 'foghorn'
Packages required but not available: 'dplyr', 'ggplot2', 'tibble'

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

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

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', 'devtools'

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

Packages suggested but not available for checking:
  'dplyr', 'ggrepel', 'testthat', 'tidyr', 'usethis', 'vdiffr', 'xgxr',
  'pillar', 'tibble', 'devtools', 'patchwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'pkgload', 'testthat', 'unix'
Packages required but not available: 'readr', 'dplyr', 'tidyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'GEOmap'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'area.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespace in Imports field not imported from: 'spanel'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'sf', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'R6' 'mgcv'
  All declared Imports should be used.
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > # /usr/bin/r
  > #
  > # Copyright 2015-2016 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > #
  > # This file is part of sadists.
  > #
  > # sadists 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.
  > #
  > # sadists 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 sadists.  If not, see <http://www.gnu.org/licenses/>.
  > #
  > # Created: 2016.01.04
  > # Copyright: Steven E. Pav, 2016
  > # Author: Steven E. Pav <shabbychef@gmail.com>
  > # Comments: Steven E. Pav
  > 
  > # because Hadley says it should be like this.
  > # see https://github.com/hadley/devtools/wiki/Testing
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'sadists.Rnw' using knitr
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Loading required package: grid
Loading required package: polynom
Quitting from lines 409-415 (sadists.Rnw) 
Error: processing vignette 'sadists.Rnw' failed with diagnostics:
could not find function "ggplot"
--- failed re-building 'sadists.Rnw'

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

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

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

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

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

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', 'haven', 'tidyr'

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

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', 'devtools', 'GGally', 'car', 'dplyr', 'tibble',
  'ggiraphExtra'

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

--- re-building 'recreating_analyses.Rmd' using rmarkdown
Quitting from lines 13-23 (recreating_analyses.Rmd) 
Error: processing vignette 'recreating_analyses.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'recreating_analyses.Rmd'

SUMMARY: processing the following file failed:
  'recreating_analyses.Rmd'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'charlatan', 'testthat', 'tibble'
Package unavailable to check Rd xrefs: 'charlatan'
Error(s) in re-building vignettes:
--- re-building 'UsingSAMBA.Rmd' using rmarkdown
Using average prevalence to calculate marginal c
Using average prevalence to calculate marginal c
Using average prevalence to calculate marginal c
Using average prevalence to calculate marginal c
Using average prevalence to calculate marginal c
Using average prevalence to calculate marginal c
Using average prevalence to calculate marginal c
Using average prevalence to calculate marginal c
Quitting from lines 272-274 (UsingSAMBA.Rmd) 
Error: processing vignette 'UsingSAMBA.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'UsingSAMBA.Rmd'

SUMMARY: processing the following file failed:
  'UsingSAMBA.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'ggplot2', 'lintr'
Errors in running code in vignettes:
when running code in 'sc-intro.Rnw'

> dir.create("Figures", showWarnings = FALSE)

> capture.output(source("Code/ex-compare-samplers.Rfrag"), 
+     file = "Figures/ex-compare-samplers.txt")
Simulation started at 2021-08-05 02:44:56.
N2,rho=0.7 Adaptive Metropolis: 557 (156,Inf) evals tuning=0.1; act.y=92.7
N2,rho=0.7 ARMS: 676 (294,9.87e+03) evals tuning=0.1; act.y=5.93
Gamma2 Adaptive Metropolis: 649 (155,Inf) evals tuning=0.1; act.y=9.88
Gamma2 ARMS: 17.8 (11.1,32.3) evals tuning=0.1; act.y=2.01
N2,rho=0.7 Adaptive Metropolis: 13.3 (8.53,21.8) evals tuning=1; act.y=6.6
N2,rho=0.7 ARMS: 656 (288,4.41e+04) evals tuning=1; act.y=9.88
Gamma2 Adaptive Metropolis: 65.8 (25.6,Inf) evals tuning=1; act.y=9.42
Gamma2 ARMS: 7.01 (5.17,9.83) evals tuning=1; act.y=1.29
N2,rho=0.7 Adaptive Metropolis: 250 (69.6,Inf) evals tuning=10; act.y=44.8
N2,rho=0.7 ARMS: 2.73e+03 (893,Inf) evals tuning=10; act.y=28.4
Gamma2 Adaptive Metropolis: 76.2 (35.8,Inf) evals tuning=10; act.y=3.16
Gamma2 ARMS: 12.7 (9.13,16.9) evals tuning=10; act.y=0.999
N2,rho=0.7 Adaptive Metropolis: NA (NA,NA) evals tuning=100; act.y=NA
N2,rho=0.7 ARMS: 1.34e+03 (530,Inf) evals tuning=100; act.y=15
Gamma2 Adaptive Metropolis: 644 (154,Inf) evals tuning=100; act.y=96.5
Gamma2 ARMS: 12.2 (9.13,16.3) evals tuning=100; act.y=0.94
Simulation finished at 2021-08-05 02:45:00.

> capture.output(source("Code/ex-compare-results.Rfrag"), 
+     file = "Figures/ex-compare-results.txt")

> pdf("Figures/ex-comparison-plot.pdf", height = 4, 
+     width = 4)

> print(comparison.plot(sampler.comparison, base_size = 8))

  When sourcing 'sc-intro.R':
Error: there is no package called 'ggplot2'
Execution halted

  'glue.Rnw'... OK
  'sc-intro.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'glue.Rnw' using Sweave
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'glue.Rnw'

--- re-building 'sc-intro.Rnw' using Sweave
Simulation started at 2021-08-05 02:45:05.
N2,rho=0.7 Adaptive Metropolis: 557 (156,Inf) evals tuning=0.1; act.y=92.7
N2,rho=0.7 ARMS: 676 (294,9.87e+03) evals tuning=0.1; act.y=5.93
Gamma2 Adaptive Metropolis: 649 (155,Inf) evals tuning=0.1; act.y=9.88
Gamma2 ARMS: 17.8 (11.1,32.3) evals tuning=0.1; act.y=2.01
N2,rho=0.7 Adaptive Metropolis: 13.3 (8.53,21.8) evals tuning=1; act.y=6.6
N2,rho=0.7 ARMS: 656 (288,4.41e+04) evals tuning=1; act.y=9.88
Gamma2 Adaptive Metropolis: 65.8 (25.6,Inf) evals tuning=1; act.y=9.42
Gamma2 ARMS: 7.01 (5.17,9.83) evals tuning=1; act.y=1.29
N2,rho=0.7 Adaptive Metropolis: 250 (69.6,Inf) evals tuning=10; act.y=44.8
N2,rho=0.7 ARMS: 2.73e+03 (893,Inf) evals tuning=10; act.y=28.4
Gamma2 Adaptive Metropolis: 76.2 (35.8,Inf) evals tuning=10; act.y=3.16
Gamma2 ARMS: 12.7 (9.13,16.9) evals tuning=10; act.y=0.999
N2,rho=0.7 Adaptive Metropolis: NA (NA,NA) evals tuning=100; act.y=NA
N2,rho=0.7 ARMS: 1.34e+03 (530,Inf) evals tuning=100; act.y=15
Gamma2 Adaptive Metropolis: 644 (154,Inf) evals tuning=100; act.y=96.5
Gamma2 ARMS: 12.2 (9.13,16.3) evals tuning=100; act.y=0.94
Simulation finished at 2021-08-05 02:45:09.

Error: processing vignette 'sc-intro.Rnw' failed with diagnostics:
 chunk 1 
Error in loadNamespace(x) : there is no package called 'ggplot2'

--- failed re-building 'sc-intro.Rnw'

SUMMARY: processing the following file failed:
  'sc-intro.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'systemfit'

Package suggested but not available for checking: 'Ecdat'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'car', 'ergm', 'ggplot2', 'network', 'networkDynamic', 'sna'
Packages suggested but not available for checking: 'AER', 'car', 'geepack'
Errors in running code in vignettes:
when running code in 'sandwich-CL.Rnw'

> library("sandwich")

> library("geepack")

  When sourcing 'sandwich-CL.R':
Error: there is no package called 'geepack'
Execution halted
when running code in 'sandwich-OOP.Rnw'

> library("AER")

  When sourcing 'sandwich-OOP.R':
Error: there is no package called 'AER'
Execution halted

  'sandwich-CL.Rnw'... failed
  'sandwich-OOP.Rnw'... failed
  'sandwich.Rnw'... OK
Error(s) in re-building vignettes:
--- re-building 'sandwich-CL.Rnw' using Sweave

Error: processing vignette 'sandwich-CL.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("geepack") : there is no package called 'geepack'

--- failed re-building 'sandwich-CL.Rnw'

--- re-building 'sandwich-OOP.Rnw' using Sweave

Error: processing vignette 'sandwich-OOP.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("AER") : there is no package called 'AER'

--- failed re-building 'sandwich-OOP.Rnw'

--- re-building 'sandwich.Rnw' using Sweave

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'sandwich.Rnw'

SUMMARY: processing the following files failed:
  'sandwich-CL.Rnw' 'sandwich-OOP.Rnw'

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

Package suggested but not available for checking: 'openair'

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

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', 'tidyverse'
Packages required but not available: 'fmtr', 'libr', 'reporter'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'maptools'
  All declared Imports should be used.
Package required but not available: 'twang'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'httptest', 'ggplot2', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'MMR_Distribution.Rmd' using rmarkdown
Quitting from lines 16-24 (MMR_Distribution.Rmd) 
Error: processing vignette 'MMR_Distribution.Rmd' failed with diagnostics:
there is no package called 'httptest'
--- failed re-building 'MMR_Distribution.Rmd'

SUMMARY: processing the following file failed:
  'MMR_Distribution.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'pvclust'
  All declared Imports should be used.
Packages required but not available: 'car', 'kableExtra', 'readxl'

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

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

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

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

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

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

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

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'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'scDIFtest.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'rvest', 'tidygraph', 'ggraph', 'ggplot2'

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: 'ez'
Package unavailable to check Rd xrefs: 'ez'
Packages required but not available:
  'dplyr', 'ggplot2', 'tibble', 'tidyr', '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:
  'dplyr', 'forcats', 'ggplot2', 'gghalves', 'tibble', 'tidyr'

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

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'Seurat', 'GSVA', 'gprofiler2', 'ADAPTS'

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', 'alakazam', 'shazam', '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'

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: 'dplyr'

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: 'forcats', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Matrix' 'pracma'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'dynutils', 'dynwrap', 'ggplot2', 'lmds', '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', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'fields'
Packages required but not available: 'AER', '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', 'lintr', 'devtools', 'roxygen2'
Running examples in 'scriptexec-Ex.R' failed
The error most likely occurred in:

> ### Name: execute
> ### Title: Executes a script and returns the output. The stdout and stderr
> ###   are captured and returned. In case of errors, the exit code will
> ###   return in the status field.
> ### Aliases: execute
> 
> ### ** Examples
> 
> library('scriptexec')
> library('testthat')
Error in library("testthat") : there is no package called 'testthat'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'scriptexec.Rmd' using rmarkdown
Quitting from lines 24-62 (scriptexec.Rmd) 
Error: processing vignette 'scriptexec.Rmd' failed with diagnostics:
there is no package called 'testthat'
--- failed re-building 'scriptexec.Rmd'

SUMMARY: processing the following file failed:
  'scriptexec.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'RCy3', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'scriptuRs-Ex.R' failed
The error most likely occurred in:

> ### Name: kjv_bible
> ### Title: Tidy data frame of the King James Version of the Bible
> ### Aliases: kjv_bible
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Packages required but not available: 'ggplot2', 'TPEA', 'ggthemes', 'Hmisc'

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', 'rgbif', 'sf', 'mapview', 'rworldmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'methods' 'pbapply' 'utils'
  All declared Imports should be used.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'testthat'

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

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

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: 'ggExtra', 'ggplot2', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'SDaA_using_survey.Rnw' using Sweave
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

The following object is masked from 'package:graphics':

    dotchart


Error: processing vignette 'SDaA_using_survey.Rnw' failed with diagnostics:
 chunk 24 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'SDaA_using_survey.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'mapview'

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

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

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

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'testthat'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'blockCV', 'readxl', 'sf', 'shinyFiles', 'SSDM',
  'ggcorrplot', 'ggplot2', 'cowplot', 'haven', 'dplyr', 'tidyr'
Running examples in 'sdmApp-Ex.R' failed
The error most likely occurred in:

> ### Name: sdmApp_PA
> ### Title: Plot presence/absence map
> ### Aliases: sdmApp_PA
> 
> ### ** Examples
> 
> r <- raster::raster(system.file("extdata","AETI.tif",package = "sdmApp"))
> r <- r > 4000
> sdmApp_PA(r)
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: sdmApp_PA ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Namespace in Imports field not imported from: 'gbm'
  All declared Imports should be used.
Running examples in 'sdmpredictors-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_correlation
> ### Title: Plot the correlation matrix for the provided layercodes
> ### Aliases: plot_correlation
> 
> ### ** Examples
> 
> correlation <- layers_correlation(c("BO_calcite", "BO_damin", "MS_bathy_5m"))
> p <- plot_correlation(correlation)
Error: ggplot2 needed for the 'plot_correlation' function to work. Please install it.
Execution halted
Package required but not available: 'ggplot2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'roxygen2'
Errors in running code in vignettes:
when running code in 'sdmvspecies.Rnw'

> options(width = 60)

> set.seed(0)

> library("sdmvspecies")

> library("raster")
Loading required package: sp

> package.dir <- system.file(package = "sdmvspecies")

> env.dir <- paste(package.dir, "/external/env", sep = "")

> files <- list.files(path = env.dir, pattern = "*.bil$", 
+     full.names = TRUE)

> env.stack <- raster::stack(files)

> print(files)
[1] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 

> config <- list(c("bio1", "1", 2), c("bio12", "2", 
+     2), c("bio5", "3", 1), c("bio7", "4", 2))

> species.raster <- nicheSynthese(env.stack, config)

> species.raster <- rescale(species.raster)

> plot(species.raster > 0.7)

> library("ggplot2")

  When sourcing 'sdmvspecies.R':
Error: there is no package called 'ggplot2'
Execution halted

  'sdmvspecies.Rnw' using 'UTF-8'... failed
Error(s) in re-building vignettes:
--- re-building 'sdmvspecies.Rnw' using Sweave
Loading required package: sp
[1] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sdmvspecies/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 

Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
 chunk 3 (label = bell_shaped_response_function) 
Error in library("ggplot2") : there is no package called 'ggplot2'

--- failed re-building 'sdmvspecies.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'spsurvey'

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: 'googleAuthR'

Package suggested but not available for checking: 'testthat'

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

Package suggested but not available for checking: 'waterData'

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

Package suggested but not available for checking: 'secrlinear'

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

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

Package suggested but not available for checking: 'secrdesign'

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

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

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

Package suggested but not available for checking: 'testthat'

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

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

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

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

Packages suggested but not available for checking:
  'testthat', 'quanteda.textmodels'

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

Package suggested but not available for checking: 'roxygen2'

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

Package suggested but not available for checking: 'rsbml'

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

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

Packages suggested but not available for checking:
  'brms', 'dplyr', 'ggraph', 'ggrepel', 'qqplotr', 'rstanarm',
  'tidygraph', 'tidyr', 'testthat', 'vdiffr'

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

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

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', 'leaflet', 'moveHMM', 'devtools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages unavailable to check Rd xrefs: 'flowClust', 'flowMerge'
Packages suggested but not available for checking:
  'testthat', 'tidyr', 'tibble', 'dplyr'
Packages required but not available:
  'dplyr', 'arm', 'patchwork', 'ggpubr', 'ggplot2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mixOmics'
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'FD'
  All declared Imports should be used.
Packages required but not available: 'semPlot', 'dplyr'

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

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

Packages which this enhances but not available for checking:
  'semPlot', 'vdiffr'
Packages required but not available: 'leaflet', 'urlshorteneR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'SemNetCleaner'
Packages required but not available:
  'dplyr', 'ggplot2', 'qgraph', 'car', 'broom', 'philentropy'

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

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

Package suggested but not available for checking: 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'semPLS-intro.Rnw' using Sweave
Loading required package: lattice

Error: processing vignette 'semPLS-intro.Rnw' failed with diagnostics:
 chunk 33 (label = sem2) 
Error in library("sem", pos = which(search() == "package:semPLS") + 1) : 
  there is no package called 'sem'

--- failed re-building 'semPLS-intro.Rnw'

SUMMARY: processing the following file failed:
  'semPLS-intro.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'mi'

Package suggested but not available for checking: 'DiagrammeR'

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

> ### Name: combinequark
> ### Title: Combine the results from the quark function
> ### Aliases: combinequark
> 
> ### ** Examples
> 
> 
> set.seed(123321)
> dat <- HolzingerSwineford1939[,7:15]
> misspat <- matrix(runif(nrow(dat) * 9) < 0.3, nrow(dat))
> dat[misspat] <- NA
> dat <- cbind(HolzingerSwineford1939[,1:3], dat)
> 
> quark.list <- quark(data = dat, id = c(1, 2))
Data Check Passed.
ID Check Passed.
Loading required namespace: mice
Failed with error:  'there is no package called 'mice''
The quark function requires the "mice" package to be installed.
> 
> final.data <- combinequark(quark = quark.list, percent = 80)
Error in if (pct[i] >= percent) { : argument is of length zero
Calls: combinequark
Execution halted
Packages required but not available: 'OpenMx', 'ggplot2', 'tidyr'

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

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

Packages suggested but not available for checking:
  'leaflet', 'leafpm', 'mapedit', 'shinyFiles', 'httptest', 'testthat'

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

Package suggested but not available for checking: 'ggExtra'

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

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

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', 'quanteda', 'RcppParallel'

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

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

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

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

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

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

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

Packages suggested but not available for checking:
  'FactoMineR', 'GDAtools', 'TraMineRextras', 'WeightedCluster',
  'questionr', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat);
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'GenomicAlignments', 'Rsamtools'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## follow http://adv-r.had.co.nz/Testing.html
  > print(sprintf("Test seqminer [version %s]", packageVersion("seqminer")))
  [1] "Test seqminer [version 8.0]"
  > print("Platform")
  [1] "Platform"
  > print(str(.Platform))
  List of 8
   $ OS.type   : chr "windows"
   $ file.sep  : chr "/"
   $ dynlib.ext: chr ".dll"
   $ GUI       : chr "RTerm"
   $ endian    : chr "little"
   $ pkgType   : chr "win.binary"
   $ path.sep  : chr ";"
   $ r_arch    : chr "x64"
  NULL
  > 
  > print("Sys.info()")
  [1] "Sys.info()"
  > print(Sys.info())
         sysname        release        version       nodename        machine 
       "Windows"   "Server x64"  "build 20348"        "FRODO"       "x86-64" 
           login           user effective_user 
         "tomas"        "tomas"        "tomas" 
  > 
  > print(citation("seqminer"))
  
  Zhan X, Liu D (2015). "SEQMINER: An R-Package to Facilitate the
  Functional Interpretation of Sequence-Based Associations." _Genetic
  Epidemiology_, *39*(8), 1242. doi: 10.1002/gepi.21918 (URL:
  https://doi.org/10.1002/gepi.21918), seqminer version 8.0, <URL:
  http://dx.doi.org/10.1002/gepi.21918>.
  
  A BibTeX entry for LaTeX users is
  
    @Article{,
      title = {SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations},
      author = {Xiaowei Zhan and Dajiang J Liu},
      journal = {Genetic Epidemiology},
      volume = {39},
      number = {8},
      pages = {1242},
      year = {2015},
      note = {seqminer version 8.0},
      web = {http://seqminer.genomic.codes},
      publisher = {Wiley Online Library},
      url = {http://dx.doi.org/10.1002/gepi.21918},
      doi = {10.1002/gepi.21918},
    }
  
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running 'sequences-test.R'
  Comparing 'sequences-test.Rout' to 'sequences-test.Rout.save' ... OK
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'dbplyr', 'readr', 'tibble'

Package suggested but not available for checking: 'DBItest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'GA', 'testthat', 'dendextend', 'ggplot2'
Package unavailable to check Rd xrefs: 'GA'
Packages suggested but not available for checking: 'testthat', 'Hmisc'
Package required but not available: 'do'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'plotly'
Packages required but not available:
  'cowplot', 'ggplot2', 'ggrepel', 'ggridges', 'patchwork', 'plotly',
  'scattermore', 'sctransform', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'MAST', 'DESeq2', 'rtracklayer', 'monocle', 'enrichR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Package suggested but not available for checking: 'mlogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'kableExtra', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggraph', 'ggplot2', 'pkgdown', 'testthat', 'tidygraph', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sf', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'geometries'
  All declared Imports should be used.
Packages required but not available:
  'dplyr', 'lwgeom', 'sf', 'tibble', 'tidygraph'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'plotly', 'tidyr'
Running examples in 'sfo-Ex.R' failed
The error most likely occurred in:

> ### Name: sfo_passengers
> ### Title: SFO Airport Air Traffic Passenger Statistics
> ### Aliases: sfo_passengers
> ### Keywords: SFO airline datasets passengers timeseries
> 
> ### ** Examples
> 
> data(sfo_passengers)
> 
> require(dplyr)
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'dplyr'
> 
> # Get summary of total number of passengers by activity type
> # in most recent month
> sfo_passengers %>%
+   filter(activity_period == max(activity_period)) %>%
+   group_by(activity_type_code) %>%
+   summarise(total = sum(passenger_count), .groups = "drop")
Error in sfo_passengers %>% filter(activity_period == max(activity_period)) %>%  : 
  could not find function "%>%"
Execution halted
Error(s) in re-building vignettes:
--- re-building 'v1_intro.Rmd' using rmarkdown
--- finished re-building 'v1_intro.Rmd'

--- re-building 'v3_analyzing_landing.Rmd' using rmarkdown
Quitting from lines 30-37 (v3_analyzing_landing.Rmd) 
Error: processing vignette 'v3_analyzing_landing.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'v3_analyzing_landing.Rmd'

SUMMARY: processing the following file failed:
  'v3_analyzing_landing.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'lwgeom', 'mapview', 'pillar', 'stars',
  'testthat', 'tibble', 'tidyr', 'tmap'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/sf/sf.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'ggplot2', 'viridis'
Package which this enhances but not available for checking: 'Hmisc'
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'tidyr'

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: 'SGP'
Error(s) in re-building vignettes:
--- re-building 'SGPdata.Rmd' using rmarkdown
Quitting from lines 2-11 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
there is no package called 'toOrdinal'
--- failed re-building 'SGPdata.Rmd'

SUMMARY: processing the following file failed:
  'SGPdata.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'plotly', 'randomNames', 'toOrdinal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'shapeNA-Ex.R' failed
The error most likely occurred in:

> ### Name: barplot.shapeNA
> ### Title: Barplot Showcasing Missingness Proportion of the Original Data
> ### Aliases: barplot.shapeNA
> 
> ### ** Examples
> 
>     S <- toeplitz(seq(1, 0.1, length.out = 3))
>     x <- mvtnorm::rmvt(100, S, df = 5)
>     y <- mice::ampute(x, mech='MCAR')$amp
Error in loadNamespace(x) : there is no package called 'mice'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'ggplot2', 'ggforce', 'ggExtra', 'ggpubr'

Package suggested but not available for checking: 'lightgbm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyverse', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'DALEX', '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', 'roxygen2', 'ggplot2', 'caret'
Error(s) in re-building vignettes:
--- re-building 'understanding_shapr.Rmd' using rmarkdown
Quitting from lines 241-282 (understanding_shapr.Rmd) 
Error: processing vignette 'understanding_shapr.Rmd' failed with diagnostics:
ggplot2 is not installed. Please run install.packages('ggplot2')
--- failed re-building 'understanding_shapr.Rmd'

SUMMARY: processing the following file failed:
  'understanding_shapr.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright 2013 Steven E. Pav. All Rights Reserved.
  > # Author: Steven E. Pav
  > 
  > # This file is part of SharpeR.
  > #
  > # SharpeR 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.
  > #
  > # SharpeR 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 SharpeR.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > # env var:
  > # nb: 
  > # see also:
  > # todo:
  > # changelog: 
  > #
  > # Created: 2013.03.14
  > # Copyright: Steven E. Pav, 2012-2013
  > # Author: Steven E. Pav
  > # Comments: Steven E. Pav
  > # SVN: $Id: blankheader.txt 25454 2012-02-14 23:35:25Z steven $
  > 
  > # 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: 'Hmisc'

Packages suggested but not available for checking:
  'spdep', 'rvest', 'dendextend', 'testthat', 'hydromad', 'daymetr',
  'elevatr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'get_started.Rmd' using rmarkdown
Quitting from lines 21-25 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'get_started.Rmd'

SUMMARY: processing the following file failed:
  'get_started.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'ggplot2', 'alakazam', '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', 'tidyr', 'ggExtra', 'ggridges', 'Hmisc'

Packages suggested but not available for checking: 'testthat', 'GGally'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggpubr', 'tidyr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly'

Packages suggested but not available for checking: 'pkgdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'shinyaframe-Ex.R' failed
The error most likely occurred in:

> ### Name: aDataScene
> ### Title: A-Frame Scene with R data
> ### Aliases: aDataScene
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'testthat', 'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'brms', 'rstan'

Packages suggested but not available for checking:
  'ggplot2', 'shinystan', 'rstanarm', 'testthat', 'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'styler'
Package required but not available: 'plotly'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'reactable'
  All declared Imports should be used.
Packages required but not available:
  'heatmaply', 'plotly', 'dplyr', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'markdown'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'googleLanguageR', 'testthat'
Packages required but not available:
  'difNLR', 'dplyr', 'ggdendro', 'ggplot2', 'plotly', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'highcharter'
Running examples in 'shinyjqui-Ex.R' failed
The error most likely occurred in:

> ### Name: Interactions
> ### Title: Mouse interactions
> ### Aliases: Interactions jqui_draggable jqui_droppable jqui_resizable
> ###   jqui_selectable jqui_sortable
> 
> ### ** Examples
> 
> library(shiny)
> library(highcharter)
Error in library(highcharter) : there is no package called 'highcharter'
Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'vroom'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'billboarder'

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'

Packages suggested but not available for checking:
  'testthat', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'plotly', 'sparklyr', 'tidyr', '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:
  'cli', 'testthat', 'apexcharter', 'ggplot2', 'dplyr'
Packages required but not available: 'dplyr', 'RDML', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'styler', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'mockery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'shiny' 'shinyjs'
  All declared Imports should be used.
Packages required but not available: 'pivottabler', 'colourpicker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggthemes', 'Epi'
Packages required but not available:
  'shinyFiles', 'colourpicker', 'plotly', 'ggplot2', 'styler', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'shinytest'
Packages required but not available:
  'recipes', 'dplyr', 'tidyr', 'esquisse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'dbplyr', 'googlesheets4'

Packages suggested but not available for checking: 'googledrive', 'gmailr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'tibble', 'testthat', 'lintr', 'leaflet', 'plotly'
Packages required but not available:
  'bayesplot', 'colourpicker', 'ggplot2', 'rstan'

Packages suggested but not available for checking: 'rstanarm', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'custom-input-extensions.Rmd' using rmarkdown
Quitting from lines 11-17 (custom-input-extensions.Rmd) 
Error: processing vignette 'custom-input-extensions.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'custom-input-extensions.Rmd'

--- re-building 'get-survey-data.Rmd' using rmarkdown
--- finished re-building 'get-survey-data.Rmd'

--- re-building 'surveying-shinysurveys.Rmd' using rmarkdown
Quitting from lines 11-16 (surveying-shinysurveys.Rmd) 
Error: processing vignette 'surveying-shinysurveys.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'surveying-shinysurveys.Rmd'

SUMMARY: processing the following files failed:
  'custom-input-extensions.Rmd' 'surveying-shinysurveys.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'readr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'parsedate', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'R6' 'shiny'
  All declared Imports should be used.
Packages required but not available: 'ypr', 'dplyr', 'readr', '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: 'StatMatch'
Packages required but not available: 'ggplot2', 'tidyr'

Package suggested but not available for checking: 'MplusAutomation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'LambertW', 'tidyr', 'ggplot2'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'hdrcde'

Depends: includes the non-default packages:
  'hdrcde', 'coda', 'MASS', 'bayesm', 'mnormt', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'hdrcde', 'tidyr', 'dplyr', 'ggplot2'

Packages suggested but not available for checking: 'tidyverse', 'viridis'

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: 'cowplot', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'tibble', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'cli'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'network', 'ggmap', 'ggplot2'

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:
  'ggplot2', 'testthat', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'car', 'ggplot2', 'kableExtra', 'readxl'
Error(s) in re-building vignettes:
--- re-building 'MoosePopR-SightabilityPopR-Demo.Rmd' using rmarkdown
Quitting from lines 17-29 (MoosePopR-SightabilityPopR-Demo.Rmd) 
Error: processing vignette 'MoosePopR-SightabilityPopR-Demo.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building 'MoosePopR-SightabilityPopR-Demo.Rmd'

--- re-building 'RatioEstimator.pdf.asis' using asis
--- finished re-building 'RatioEstimator.pdf.asis'

--- re-building 'SightabilityModel.Rnw' using Sweave
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'SightabilityModel.Rnw'

SUMMARY: processing the following file failed:
  'MoosePopR-SightabilityPopR-Demo.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'cli', 'cowplot', 'dplyr', 'ggplot2', 'ggpubr', 'NMF', 'tidyr'

Packages suggested but not available for checking:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19', 'ggalluvial',
  'ggcorrplot', 'ggfittext', 'ggplotify', 'ggrepel', 'patchwork',
  'roxygen2', 'testthat', 'tibble', 'UCSCXenaTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'sigmoid.Rmd' using rmarkdown
Quitting from lines 59-67 (sigmoid.Rmd) 
Error: processing vignette 'sigmoid.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'sigmoid.Rmd'

SUMMARY: processing the following file failed:
  'sigmoid.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rsamtools', 'Seurat', 'dplyr', 'ggplot2', 'ggseqlogo', 'tidyr',
  'patchwork', 'ggrepel', 'ggforce'

Packages suggested but not available for checking:
  'testthat', 'chromVAR', 'TFBSTools', 'motifmatchr', 'BSgenome',
  'rtracklayer', 'biovizBase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'Seurat'

Package suggested but not available for checking: 'rhdf5'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggraph'
Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'ggrepel', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'signs.Rmd' using rmarkdown
Quitting from lines 18-23 (signs.Rmd) 
Error: processing vignette 'signs.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'signs.Rmd'

SUMMARY: processing the following file failed:
  'signs.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'biclust', 'GSVA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'phylobase', 'phyext2', 'phyloseq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'qpdf'
  All declared Imports should be used.
Packages required but not available: 'sf', 'ggplot2', 'ggforce'

Package suggested but not available for checking: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'gibble', 'tibble', 'unjoin'

Packages suggested but not available for checking:
  'testthat', 'trip', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'car', 'ggplot2', 'tidyverse', 'tibble', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'ggplot2', 'tidyr'

Packages suggested but not available for checking: 'GGally', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SimMultiCorrData', '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', 'sessioninfo'

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', 'broom'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr', 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'pkgdown', 'testthat', 'kableExtra', 'ggplot2', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'bde'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'arm', 'ggplot2', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'DiagrammeR', '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:
  'simmer.plot', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Copyright (C) 2014 Bart Smeets
  > # Copyright (C) 2015-2016,2018 Iñaki Ucar
  > #
  > # This file is part of simmer.
  > #
  > # simmer 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.
  > #
  > # simmer 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 simmer. If not, see <http://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'BSgenome'

Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg38'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'viridis', 'bayesplot'

Packages suggested but not available for checking: 'readxl', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'quadprog'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'forcats', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ggplot2', 'leaflet', 'leafpop',
  'leaflet.extras', 'plotly', 'readr', 'sf', 'tibble', 'tidyr',
  'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'broom'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'sjstats', 'cccrm'

Packages suggested but not available for checking:
  'testthat', 'tidyverse', 'readr', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'VIM', 'EnvStats'

Packages suggested but not available for checking:
  'haven', 'testthat', 'surveysd'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'dplyr', 'VIM'
Package unavailable to check Rd xrefs: 'VIM'
Package required but not available: 'ShortRead'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'moveHMM', 'testthat'
Packages required but not available: 'pbkrtest', 'car'

Packages suggested but not available for checking: 'testthat', 'lmerTest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'SimRVPedigree', 'dplyr'

Packages suggested but not available for checking: 'vcfR', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'OpenMx'
Package required but not available: 'nlist'

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:
  'ggplot2', 'dplyr', 'tidyr', 'forcats', 'testthat', 'badger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'hedgehog', 'testthat'
Running examples in 'simstudy-Ex.R' failed
The error most likely occurred in:

> ### Name: addCondition
> ### Title: Add a single column to existing data set based on a condition
> ### Aliases: addCondition
> 
> ### ** Examples
> 
> 
> # New data set
> 
> def <- defData(varname = "x", dist = "categorical", formula = ".33;.33")
> def <- defData(def, varname = "y", dist = "uniform", formula = "-5;5")
> 
> dt <- genData(1000, def)
Warning: Probabilities do not sum to 1. Adding category to all rows!
> 
> # Define conditions
> 
> defC <- defCondition(
+   condition = "x == 1", formula = "5 + 2*y-.5*y^2",
+   variance = 1, dist = "normal"
+ )
> defC <- defCondition(defC,
+   condition = "x == 2",
+   formula = "3 - 3*y + y^2", variance = 2, dist = "normal"
+ )
> defC <- defCondition(defC,
+   condition = "x == 3",
+   formula = "abs(y)", dist = "poisson"
+ )
> 
> # Add column
> 
> dt <- addCondition(defC, dt, "NewVar")
> 
> # Plot data
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Package required but not available: 'plotly'

Packages suggested but not available for checking:
  'fields', 'viridis', 'ggplot2', 'INLA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'flexsurv'
Error(s) in re-building vignettes:
--- re-building 'simsurv_technical.Rmd' using rmarkdown
--- finished re-building 'simsurv_technical.Rmd'

--- re-building 'simsurv_usage.Rmd' using rmarkdown
Quitting from lines 15-23 (simsurv_usage.Rmd) 
Error: processing vignette 'simsurv_usage.Rmd' failed with diagnostics:
there is no package called 'flexsurv'
--- failed re-building 'simsurv_usage.Rmd'

SUMMARY: processing the following file failed:
  'simsurv_usage.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking: 'ggplot2', 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'crqa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'rematch2'

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'

Packages suggested but not available for checking:
  'ggplot2', 'purrrlyr', 'testthat', 'kableExtra'

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', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'pracma'
  All declared Imports should be used.
Packages required but not available:
  'PNADcIBGE', 'POFIBGE', 'PNSIBGE', 'COVIDIBGE', 'tidyverse', 'cli',
  'tibble'

Packages suggested but not available for checking:
  'readr', 'dplyr', 'projmgr', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'systemfit', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'miceadds'
Packages required but not available: 'dplyr', 'tidyr', 'ggpubr', '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', 'forcats', 'ggplot2', 'rsample', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'hyfo', '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: 'dplyr', 'ymlthis'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'big_crush_test.Rmd' using rmarkdown
--- finished re-building 'big_crush_test.Rmd'

--- re-building 'sitmo_internals.Rmd' using rmarkdown
--- finished re-building 'sitmo_internals.Rmd'

--- re-building 'uniform_rng_with_sitmo.Rmd' using rmarkdown
Quitting from lines 130-154 (uniform_rng_with_sitmo.Rmd) 
Error: processing vignette 'uniform_rng_with_sitmo.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'uniform_rng_with_sitmo.Rmd'

SUMMARY: processing the following file failed:
  'uniform_rng_with_sitmo.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'sitree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'SiZer-Ex.R' failed
The error most likely occurred in:

> ### Name: Arkansas
> ### Title: Time Series of Macroinvertabrates Abundance in the Arkansas
> ###   River.
> ### Aliases: Arkansas
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 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'
> 
> data(Arkansas)
> ggplot(Arkansas, aes(x=year, y=sqrt.mayflies)) + 
+    geom_point()
Error in ggplot(Arkansas, aes(x = year, y = sqrt.mayflies)) : 
  could not find function "ggplot"
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'haven', 'sjmisc', 'sjPlot', 'testthat'
Package unavailable to check Rd xrefs: 'haven'
Running examples in 'sjlabelled-Ex.R' failed
The error most likely occurred in:

> ### Name: add_labels
> ### Title: Add, replace or remove value labels of variables
> ### Aliases: add_labels replace_labels remove_labels
> 
> ### ** Examples
> 
> # add_labels()
> data(efc)
> get_labels(efc$e42dep)
[1] "independent"          "slightly dependent"   "moderately dependent"
[4] "severely dependent"  
> 
> x <- add_labels(efc$e42dep, labels = c(`nothing` = 5))
Error in get_na_helper(x, as.tag) : 
  Package 'haven' required for this function. Please install it.
Calls: add_labels ... add_labels_helper -> get_na -> get_na.default -> get_na_helper
Execution halted
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'haven', 'mice', 'sjPlot', 'sjstats', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'sjmisc', 'sjstats', 'tidyr'

Packages suggested but not available for checking:
  'brms', 'car', 'cowplot', 'ggrepel', 'ggridges', 'rstanarm',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'dplyr', 'modelr', 'sjmisc', 'tidyr'

Packages suggested but not available for checking:
  'brms', 'car', 'ggplot2', 'sjPlot', 'rstan', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'broom', 'Hmisc'

Packages suggested but not available for checking:
  'devtools', 'car', 'tibble', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'repr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'dtplyr', 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'modeltime', 'parsnip', 'rsample', 'tibble', 'tidyr',
  'tune'

Packages suggested but not available for checking:
  'ggplot2', 'recipes', 'timetk', 'workflows', 'yardstick',
  'workflowsets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'car', 'viridis', 'lmerTest', 'gt'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'GD'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'leaflet'

Packages suggested but not available for checking: 'testthat', 'kableExtra'

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', 'texPreview'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'forecast', 'imputeTS', 'TSclust', 'tsoutliers'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'RcmdrPlugin.SLC'
Packages required but not available: 'ggplot2', 'viridis', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cowplot', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggthemes', 'Hmisc', 'caret'

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:
  'agricolae', 'car', 'mosaic'
Packages suggested but not available for checking:
  'CCA', 'Hmisc', 'agricolae', 'car', 'mosaic'
Package required but not available: 'sf'

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: 'rcrossref'
Error(s) in re-building vignettes:
--- re-building 'slgf_vignette.Rmd' using rmarkdown
Quitting from lines 20-28 (slgf_vignette.Rmd) 
Error: processing vignette 'slgf_vignette.Rmd' failed with diagnostics:
there is no package called 'rcrossref'
--- failed re-building 'slgf_vignette.Rmd'

SUMMARY: processing the following file failed:
  'slgf_vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'basics.Rmd' using rmarkdown
--- finished re-building 'basics.Rmd'

--- re-building 'doms.Rmd' using rmarkdown
Quitting from lines 82-91 (doms.Rmd) 
Error: processing vignette 'doms.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building 'doms.Rmd'

--- re-building 'iframes.Rmd' using rmarkdown
--- finished re-building 'iframes.Rmd'

--- re-building 'pdfs.Rmd' using rmarkdown
--- finished re-building 'pdfs.Rmd'

--- re-building 'plots.Rmd' using rmarkdown
--- finished re-building 'plots.Rmd'

--- re-building 'shiny.Rmd' using rmarkdown
--- finished re-building 'shiny.Rmd'

--- re-building 'tests_and_coverage.Rmd' using rmarkdown
--- finished re-building 'tests_and_coverage.Rmd'

SUMMARY: processing the following file failed:
  'doms.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'rowwise.Rmd' using rmarkdown
Quitting from lines 20-22 (rowwise.Rmd) 
Error: processing vignette 'rowwise.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'rowwise.Rmd'

--- re-building 'slider.Rmd' using rmarkdown
Quitting from lines 20-23 (slider.Rmd) 
Error: processing vignette 'slider.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'slider.Rmd'

--- re-building 'tsibble.Rmd' using rmarkdown
--- finished re-building 'tsibble.Rmd'

SUMMARY: processing the following files failed:
  'rowwise.Rmd' 'slider.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'viridisLite'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'slim.Rmd' using rmarkdown
Quitting from lines 65-69 (slim.Rmd) 
Error: processing vignette 'slim.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'slim.Rmd'

SUMMARY: processing the following file failed:
  'slim.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'caret', 'testthat'
Packages required but not available: 'Hmisc', 'weights', 'candisc'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'spatstat'
  All declared Imports should be used.
Running 'test-all.R'
Running the tests in 'tests/test-all.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("smacpod")
  Error in test_check("smacpod") : could not find function "test_check"
  Execution halted
Packages suggested but not available for checking:
  'kableExtra', 'sdcHierarchies', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_SmallCountRounding.Rmd' using rmarkdown
Quitting from lines 18-52 (Introduction_to_SmallCountRounding.Rmd) 
Error: processing vignette 'Introduction_to_SmallCountRounding.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'Introduction_to_SmallCountRounding.Rmd'

SUMMARY: processing the following file failed:
  'Introduction_to_SmallCountRounding.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'RcppParallel', 'EnvStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rhdf5', 'rvest'

Packages suggested but not available for checking: 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'GGally'

Packages suggested but not available for checking:
  'testthat', 'DataExplorer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'caret', 'dplyr'
Namespace in Imports field not imported from: 'covr'
  All declared Imports should be used.
Packages required but not available:
  'spdep', 'marmap', 'ggplot2', 'caret', 'ggthemes', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vroom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sva', 'isva'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GSVA', 'samr', 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'tableone', 'dplyr'
Error(s) in re-building vignettes:
--- re-building 'smd_usage.Rmd' using rmarkdown
Quitting from lines 137-143 (smd_usage.Rmd) 
Error: processing vignette 'smd_usage.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'smd_usage.Rmd'

SUMMARY: processing the following file failed:
  'smd_usage.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'MESS'

Packages suggested but not available for checking:
  'lintr', 'testthat', 'SpatialEpi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'readme.Rmd' using rmarkdown
Quitting from lines 13-19 (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
Running 'testall.R'
Running the tests in 'tests/testall.R' failed.
Complete output:
  > library( "testthat" )
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'SMITIDstruct', 'testthat'
Packages required but not available: 'dplyr', 'tibble', 'rvest'

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', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'roxygen2', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly'

Packages suggested but not available for checking: 'testthat', 'rPython'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'demography'
Namespaces in Imports field not imported from:
  'compiler' 'lmtest'
  All declared Imports should be used.
Packages suggested but not available for checking: 'SpatialVx', 'fields'
Package required but not available: 'greybox'

Packages suggested but not available for checking:
  'Mcomp', 'testthat', 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'smovie-Ex.R' failed
The error most likely occurred in:

> ### Name: ett
> ### Title: Extremal Types Theorem (ETT)
> ### Aliases: ett
> 
> ### ** Examples
> 
> # Exponential data: xi = 0
> ett()
Error: the revdbayes package is needed. Please install it.
Execution halted
Packages required but not available: 'ggraph', 'ggplot2', 'colourpicker'

Package suggested but not available for checking: 'ggforce'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'tibble', 'purrrlyr'
Warnings in file 'R/replace_special_characters_internal.R':
  unable to translate '<U+00C4>' to native encoding
  unable to translate '<U+00D6>' to native encoding
  unable to translate '<U+00DC>' to native encoding
  unable to translate '<U+00E4>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00FC>' to native encoding
  unable to translate '<U+00DF>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
Packages required but not available: 'dplyr', 'forcats', 'readr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rvest'

Packages suggested but not available for checking:
  'testthat', 'leaflet', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'haplo.stats', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'dplyr', 'devtools', 'usethis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'oai'

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', 'mice', 'tidycensus', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'sf', 'testthat', 'tibble', 'tigris'

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: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'arm', 'caret', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'sf', 'rvest', 'testthat', 'ggplot2', 'mapview'
Packages required but not available: 'dplyr', 'PAutilities'

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: 'tdr'
Packages suggested but not available for checking: 'tidyverse', 'rsample'
Namespaces in Imports field not imported from:
  'R6' 'lgr'
  All declared Imports should be used.
Packages required but not available: 'ggplot2', 'ggwordcloud', 'metR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'openair', 'colourpicker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
Quitting from lines 158-159 (SongEvo.Rmd) 
Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
there is no package called 'Hmisc'
--- failed re-building 'SongEvo.Rmd'

SUMMARY: processing the following file failed:
  'SongEvo.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'googleCloudStorageR', 'googleLanguageR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'SpATS'
Running examples in 'SOP-Ex.R' failed
The error most likely occurred in:

> ### Name: rae
> ### Title: Defining random effects in SOP formula
> ### Aliases: rae
> ### Keywords: models smooth regression
> 
> ### ** Examples
> 
> library(SOP)
> require(SpATS)
Loading required package: SpATS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'SpATS'
> ## An example of use of SOP package for the analysis of field trials experiments.
> ## Taken from the SpATS package.
> data(wheatdata)
Warning in data(wheatdata) : data set 'wheatdata' not found
> 
> # Create factor variable for row and columns
> wheatdata$R <- as.factor(wheatdata$row)
Error in is.factor(x) : object 'wheatdata' not found
Calls: as.factor -> is.factor
Execution halted
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'testthat', 'roxygen2', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown
Sotkanet R tools (C) 2013-2021 rOpenGov
http://ropengov.org
Quitting from lines 46-50 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- 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: 'ggplot2', 'Seurat'

Packages suggested but not available for checking: 'rstan', 'DropletUtils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'r2cytoscape'
Running examples in 'SourceSet-Ex.R' failed
The error most likely occurred in:

> ### Name: easyLookSource
> ### Title: Easy look results
> ### Aliases: easyLookSource
> 
> ### ** Examples
> 
> ## Load the SourceSetObj obtained from the source set analysis of ALL dataset
> 
> # see vignette for more details
> print(load(file=system.file("extdata","ALLsourceresult.RData",package = "SourceSet")))
[1] "results.all"
> class(results.all)
[1] "sourceSetList"
> n.primary<-length(lapply(results.all,function(x) x$primarySet))
> 
> # show only genes that appear in at least one of the source sets of the investigated pathways
> easyLookSource(sourceObj=results.all, maxnum.variable = n.primary,
+                label.variable = "Genes",label.graph = "Pathways")
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: easyLookSource ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SourceSet.Rmd' using rmarkdown
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Identifing all possible orderings..
Total run time: 1.08 secs
Quitting from lines 311-312 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'SourceSet.Rmd'

SUMMARY: processing the following file failed:
  'SourceSet.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'broom', 'dplyr', 'ggplot2', '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: 'cshapes', 'sf'
Error(s) in re-building vignettes:
--- re-building 'introduction-to-spacey.Rmd' using rmarkdown
Quitting from lines 41-42 (introduction-to-spacey.Rmd) 
Error: processing vignette 'introduction-to-spacey.Rmd' failed with diagnostics:
there is no package called 'pkgload'
--- failed re-building 'introduction-to-spacey.Rmd'

SUMMARY: processing the following file failed:
  'introduction-to-spacey.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'quanteda', 'testthat', 'tidytext', 'tibble'
Running 'spelling.R'
  Running 'testthat.R'
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: 'devtools', 'SpaDES.core'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'quickPlot', 'qs'

Packages suggested but not available for checking:
  'DiagrammeR', 'dplyr', 'ggplot2', 'googledrive', 'SpaDES.tools',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'quickPlot', 'SpaDES.core', 'SpaDES.tools'

Packages suggested but not available for checking:
  'testthat', 'SpaDES.addins'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quickPlot'

Packages suggested but not available for checking:
  'dplyr', 'googledrive', 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'earlywarnings', 'testthat'
Package unavailable to check Rd xrefs: 'earlywarnings'
Packages suggested but not available for checking: 'testthat', 'Infusion'
Running examples in 'spam-Ex.R' failed
The error most likely occurred in:

> ### Name: covmat
> ### Title: Covariance functions
> ### Aliases: covmat cov.exp cov.sph cor.sph cov.nug cov.wu1 cov.wu2 cov.wu3
> ###   cov.wend1 cov.wend2 cov.mat
> ### Keywords: algebra
> 
> ### ** Examples
> 
> set.seed(123)
> n <- 200
> locs <- cbind(runif(n),runif(n))
> h <- nearest.dist(locs, delta=sqrt(2), upper = NULL)
> Sigma <- cov.sph(h, c(.3, 1, .1))
> 
> iidsample <- rnorm(n)
> cholS <- chol.spam(as.spam(Sigma))
> iorder <- iord <- ordering(cholS, inv = TRUE)
> sample <- (iidsample %*% as.spam(cholS))[iorder]
> plot(locs, col = fields::tim.colors(n = 256)[cut(sample, n)], pch = 20)
Error in loadNamespace(x) : there is no package called 'fields'
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'ScottKnott', 'car', 'spdep', 'spatialreg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'fields', '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: 'sparklyr', '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: 'sparklyr'

Package suggested but not available for checking: 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'sparklyr', 'sparklyr.nested'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dbplyr', 'dplyr', 'sparklyr'

Package suggested but not available for checking: 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Invalid NAMESPACE file, parsing gives:
Error in utils::packageVersion("dbplyr"): there is no package called 'dbplyr'

See section 'Package namespaces' in the 'Writing R Extensions' manual.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sparklyr'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'network', 'RCy3', 'testthat'
Packages unavailable to check Rd xrefs: 'RCy3', 'network'
Package required but not available: 'refund'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'sparseHessianFD.Rnw' using knitr
kpsewhich: major issue: User/administrator updates are out-of-sync.
Quitting from lines 1270-1273 (sparseHessianFD.Rnw) 
Error: processing vignette 'sparseHessianFD.Rnw' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'sparseHessianFD.Rnw'

SUMMARY: processing the following file failed:
  'sparseHessianFD.Rnw'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ops <- options("crayon.enabled" = FALSE)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tidyverse', 'viridis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'sparseMVN.Rnw' using knitr
Quitting from lines 73-87 (sparseMVN.Rnw) 
Error: processing vignette 'sparseMVN.Rnw' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'sparseMVN.Rnw'

SUMMARY: processing the following file failed:
  'sparseMVN.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'FactoMineR', 'dplyr', 'tidyr', 'ggplot2', 'plotly', 'ggdendro',
  'explor', 'leaflet', 'mapview'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'spatstat.linnet'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'irlba' 'knitr' 'rmarkdown'
  All declared Imports should be used.
Running examples in 'SpatialBSS-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.sbss
> ### Title: Plot Method for an Object of Class 'sbss'
> ### Aliases: plot.sbss
> 
> ### ** Examples
> 
> # simulate coordinates
> coords <- runif(1000 * 2) * 20
> dim(coords) <- c(1000, 2)
> 
> # simulate random field
> if (!requireNamespace('RandomFields', quietly = TRUE)) {
+   stop('Please install the package RandomFields to run the example code.')
+ } else {
+   RandomFields::RFoptions(spConform = FALSE)
+   field_1 <- RandomFields::RFsimulate(model = RandomFields::RMexp(), 
+                                       x = coords)
+   field_2 <- RandomFields::RFsimulate(model = RandomFields::RMspheric(), 
+                                       x = coords)
+   field_3 <- RandomFields::RFsimulate(model = RandomFields::RMwhittle(nu = 2),  
+                                       x = coords)
+   field <- cbind(field_1, field_2, field_3)
+ }
> 
> # compute ring kernel matrices
> kernel_parameters <- c(0, 1, 1, 2, 2, 3)
> ring_kernel_list <- spatial_kernel_matrix(coords, 'ring', kernel_parameters)
> 
> # apply sbss SpatialPointsDataFrame object
> field_sp <- sp::SpatialPointsDataFrame(coords = coords, data = data.frame(field))
> res_sp <- sbss(field_sp, kernel_list = ring_kernel_list)
> 
> # plot with SpatialPointsDataFrame object
> plot(res_sp)
> 
> # plot with SpatialPointsDataFrame object 
> # and additional arguments for spplot function
> plot(res_sp, colorkey = TRUE, as.table = TRUE, cex = 1)
> 
> # apply sbss with sf object
> if (!requireNamespace('sf', quietly = TRUE)) {
+   stop('Please install the package sf to run the example code.')
+ } else {
+   field_sf <- sf::st_as_sf(data.frame(coords = coords, field), 
+                            coords = c(1,2))
+   res_sf <- sbss(x = field_sf, kernel_list = ring_kernel_list)
+ }
Error: Please install the package sf to run the example code.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SBSS.Rmd' using rmarkdown
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
Quitting from lines 167-176 (SBSS.Rmd) 
Error: processing vignette 'SBSS.Rmd' failed with diagnostics:
Please install the package sf to run the example code.
--- failed re-building 'SBSS.Rmd'

SUMMARY: processing the following file failed:
  'SBSS.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'sf', 'spdep'

Packages suggested but not available for checking:
  'exactextractr', 'readr', 'rms', 'EnvStats', 'GeNetIt', 'RStoolbox',
  'tabularaster'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'leaflet', 'SpatialEpi', 'spdep'

Package suggested but not available for checking: 'INLA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'spdep'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'SDraw', 'fields'

Packages suggested but not available for checking:
  'INLA', 'testthat', 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'dplyr'

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: 'spdep', 'GWmodel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'spdep'

Packages suggested but not available for checking: 'sf', 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'leafem', 'leafgl', 'leaflet', 'sf', 'tmap',
  'viridis'

Packages suggested but not available for checking: 'testthat', 'vroom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rsample', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'testthat', 'yardstick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'ggdark', 'Surrogate', 'janitor',
  'modelr', '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: 'fields'

Package suggested but not available for checking: 'OpenStreetMap'

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', 'ggplot2', 'sf', 'trip', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'LS2Wstat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'sf', 'spDataLarge', 'spdep', 'spatialreg'
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'spatialreg', 'tmap', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'separationplot'

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: 'ggplot2', 'readr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'tidyverse', 'mrbsizeR'
Package required but not available: 'xcms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'caret', 'ggplot2', 'GGally', 'speaq', 'imputeTS',
  'specmine.datasets', 'plotly'

Packages suggested but not available for checking:
  'ggdendro', 'qdap', 'MAIT', 'xcms', 'rcytoscapejs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'cowplot', 'dplyr', 'ggplot2', 'ggraph', 'tibble', 'tidyr'

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'

Packages suggested but not available for checking: 'caret', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'NMF', 'plotly', 'viridis', 'hNMF'

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', 'patrick', 'viridis'
Running examples in 'spectralGraphTopology-Ex.R' failed
The error most likely occurred in:

> ### Name: learn_bipartite_graph
> ### Title: Learn a bipartite graph Learns a bipartite graph on the basis of
> ###   an observed data matrix
> ### Aliases: learn_bipartite_graph
> 
> ### ** Examples
> 
> library(spectralGraphTopology)
> library(igraph)

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> library(viridis)
Error in library(viridis) : there is no package called 'viridis'
Execution halted
Packages required but not available: 'ggplot2', 'testthat'

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: 'ggplot2', 'ClusterR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'quadmesh'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'spdep', 'ezsim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mlr', 'ggplot2'

Package suggested but not available for checking: 'caret'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pegas'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > ## run all tests
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_check('spiders')
  Error in test_check("spiders") : could not find function "test_check"
  Execution halted
Packages required but not available: 'geepack', '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:
  'tourr', 'ggplot2', 'gganimate', 'plotly'

Packages suggested but not available for checking:
  'dplyr', 'GGally', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'cowplot', 'dendextend'
Package unavailable to check Rd xrefs: 'dendextend'
Packages suggested but not available for checking: 'testthat', 'pkgdown'
Packages required but not available: 'dplyr', 'ggplot2', 'ggsci', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mosaic', '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', 'ggplot2', 'patchwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'antaresViz'
Package unavailable to check Rd xrefs: 'antaresViz'
Packages required but not available: 'fields', 'ggplot2', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'spdep', 'sf', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgbif', 'rbison', 'rebird', 'rvertnet', 'tibble'

Packages suggested but not available for checking: 'testthat', 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Note that you would never run this file directly. This is used by tools::testInstallPackages()
  > # and other packages like covr.
  > # To actually run the tests, you need to set the working directory then run
  > # devtools::test()
  > 
  > # This line ensures that R CMD check can run tests.
  > # See https://github.com/hadley/testthat/issues/144
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(spongebob)
  > 
  > testthat::test_check('spongebob')
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'pkgdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'CausalImpact'

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', 'vdiffr', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'smoof', 'SPOT', 'plotly', 'shinyFiles'

Packages suggested but not available for checking:
  'testthat', 'shinytest', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'readr', 'rvest', 'tibble', 'janitor', 'ggridges',
  'genius'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'benchmarkme', 'ggplot2', 'ggsci', 'plotly', 'sensitivity', 'smoof',
  'SPOT', 'mlr'

Packages suggested but not available for checking:
  'babsim.hospital', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'cli', 'patchwork', 'ggrepel', 'ggExtra', 'ggbeeswarm',
  'ggplot2'

Packages suggested but not available for checking: 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly'

Packages suggested but not available for checking:
  'babsim.hospital', 'car', 'farff', 'readr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'sampling'
  All declared Imports should be used.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'gganimate', 'ggraph', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'spreval-Ex.R' failed
The error most likely occurred in:

> ### Name: catchcan
> ### Title: catch can data
> ### Aliases: catchcan
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(fields) # for easy grid construction
Error in library(fields) : there is no package called 'fields'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'lateral-move.Rmd' using rmarkdown
Quitting from lines 45-55 (lateral-move.Rmd) 
Error: processing vignette 'lateral-move.Rmd' failed with diagnostics:
there is no package called 'fields'
--- failed re-building 'lateral-move.Rmd'

--- re-building 'solid-set.Rmd' using rmarkdown
Quitting from lines 37-48 (solid-set.Rmd) 
Error: processing vignette 'solid-set.Rmd' failed with diagnostics:
there is no package called 'fields'
--- failed re-building 'solid-set.Rmd'

--- re-building 'traveling-sys.Rmd' using rmarkdown
--- finished re-building 'traveling-sys.Rmd'

SUMMARY: processing the following files failed:
  'lateral-move.Rmd' 'solid-set.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'car', 'ggplot2', 'spatialreg', 'spdep'

Packages suggested but not available for checking: 'dplyr', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'sf'

Packages suggested but not available for checking: 'testthat', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'rstantools', 'StanHeaders'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'

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: 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'GGally', 'readr', 'testthat'
Running 'run_testthat.R'
Running the tests in 'tests/run_testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'viridis', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dbplyr'

Packages suggested but not available for checking: 'testthat', 'arm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'rvest', 'polite', 'naniar', 'janitor',
  'Hmisc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'TripleR'
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'r4ss', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tsBSS', 'ICtest', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'ssc-Ex.R' failed
The error most likely occurred in:

> ### Name: coBC
> ### Title: CoBC method
> ### Aliases: coBC
> 
> ### ** Examples
> 
> 
> library(ssc)
> 
> ## Load Wine data set
> data(wine)
> 
> cls <- which(colnames(wine) == "Wine")
> x <- wine[, -cls] # instances without classes
> y <- wine[, cls] # the classes
> x <- scale(x) # scale the attributes
> 
> ## Prepare data
> set.seed(20)
> # Use 50% of instances for training
> tra.idx <- sample(x = length(y), size = ceiling(length(y) * 0.5))
> xtrain <- x[tra.idx,] # training instances
> ytrain <- y[tra.idx]  # classes of training instances
> # Use 70% of train instances as unlabeled set
> tra.na.idx <- sample(x = length(tra.idx), size = ceiling(length(tra.idx) * 0.7))
> ytrain[tra.na.idx] <- NA # remove class information of unlabeled instances
> 
> # Use the other 50% of instances for inductive testing
> tst.idx <- setdiff(1:length(y), tra.idx)
> xitest <- x[tst.idx,] # testing instances
> yitest <- y[tst.idx] # classes of testing instances
> 
> ## Example: Training from a set of instances with 1-NN as base classifier.
> set.seed(1)
> m1 <- coBC(x = xtrain, y = ytrain, 
+            learner = caret::knn3, 
+            learner.pars = list(k = 1),
+            pred = "predict")
Error in loadNamespace(x) : there is no package called 'caret'
Calls: coBC ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: 'SingleCaseES'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bigstatsr', 'chickn', 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'shinyFiles', 'spThin'

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'

Packages suggested but not available for checking:
  'testthat', 'readr', 'tidyr', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'BIGDAWG', 'dplyr', 'sessioninfo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'engine.R'
  Comparing 'engine.Rout' to 'engine.Rout.save' ...4d3
< Linking to libssh v0.9.5
  Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'tidyr', 'dplyr', 'airportr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'parsnip', 'dplyr', 'RSSL'

Packages suggested but not available for checking:
  'caret', 'tidymodels', 'testthat', 'tidyverse', 'factoextra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'rstantools', 'ggplot2', 'cowplot', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'gganimate'
Package required but not available: 'RDS'

Packages suggested but not available for checking: 'network', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'scanstatistics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggfortify', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stabledist'
  All declared Imports should be used.
Package required but not available: 'sem'

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:
  'cowplot', 'ggdendro', 'ggplot2', 'testthat'
Running examples in 'stabm-Ex.R' failed
The error most likely occurred in:

> ### Name: plotFeatures
> ### Title: Plot Selected Features
> ### Aliases: plotFeatures
> 
> ### ** Examples
> 
> feats = list(1:3, 1:4, 1:5)
> mat = 0.92 ^ abs(outer(1:10, 1:10, "-"))
> plotFeatures(features = feats)
Loading required namespace: ggplot2
Failed with error:  'there is no package called 'ggplot2''
Loading required namespace: cowplot
Failed with error:  'there is no package called 'cowplot''
Loading required namespace: ggdendro
Failed with error:  'there is no package called 'ggdendro''
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: plotFeatures ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'stabm.Rmd' using rmarkdown
Loading required namespace: ggplot2
Failed with error:  'there is no package called 'ggplot2''
Loading required namespace: cowplot
Failed with error:  'there is no package called 'cowplot''
Loading required namespace: ggdendro
Failed with error:  'there is no package called 'ggdendro''
Quitting from lines 65-66 (stabm.Rmd) 
Error: processing vignette 'stabm.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'stabm.Rmd'

SUMMARY: processing the following file failed:
  'stabm.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'tune', 'dplyr', 'tibble', 'parsnip', 'workflows', 'recipes',
  'rsample', 'workflowsets', 'butcher', 'yardstick', 'tidyr', 'dials',
  'ggplot2', 'cli'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pegas', 'adegenet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'afex', 'lmerTest', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'using-standardize.Rmd' using rmarkdown
Quitting from lines 362-367 (using-standardize.Rmd) 
Error: processing vignette 'using-standardize.Rmd' failed with diagnostics:
there is no package called 'afex'
--- failed re-building 'using-standardize.Rmd'

SUMMARY: processing the following file failed:
  'using-standardize.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'RcppParallel'

Package suggested but not available for checking: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'stapler-Ex.R' failed
The error most likely occurred in:

> ### Name: staple_bin_mat
> ### Title: STAPLE on binary matrix
> ### Aliases: staple_bin_mat
> 
> ### ** Examples
> 
> n = 5
> r = 1000
> sens = c(0.8, 0.9, 0.8, 0.5, 0.8)
> spec = c(0.9, 0.75, 0.99, 0.98, 0.92)
> suppressWarnings(RNGversion("3.5.0"))
> set.seed(20171120)
> n_1 = 200
> n_0 = r - n_1
> truth = c(rep(0, n_0), rep(1, n_1))
> pred_1 = rbinom(n = n, size = n_1, prob = sens)
> pred_0 = rbinom(n = n, size = n_0, prob = spec)
> pred_0 = sapply(pred_0, function(n) {
+    sample(c(rep(0, n), rep(1, n_0 -n)))
+ })
> pred_1 = sapply(pred_1, function(n) {
+    sample(c(rep(1, n), rep(0, n_1 -n)))
+ })
> pred = rbind(pred_0, pred_1)
> true_sens = colMeans(pred[ truth == 1, ])
> true_spec = colMeans(1-pred[ truth == 0, ])
> x = t(pred)
> staple_out = staple_bin_mat(x)
iter: 1, diff: 0.465230987394219
iter: 10, diff: 0.000389251248063993
iter: 20, diff: 6.3176305742374e-07
iter: 30, diff: 1.02407371471713e-09
iter: 40, diff: 1.65989444411707e-12
iter: 50, diff: 2.66453525910038e-15
Convergence!
> testthat::expect_equal(staple_out$sensitivity,
+ c(0.781593858553476, 0.895868301462594,
+ 0.760514086161722, 0.464483444340873,
+ 0.765239314719065))
Error in loadNamespace(x) : there is no package called 'testthat'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'ggplot2', 'eemR', 'dplyr', 'tidyr', 'tibble', 'GGally', 'drc',
  'cdom', 'readr'

Packages suggested but not available for checking: 'plotly', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages which this enhances but not available for checking:
  'AER', 'dynlm', 'erer', 'ergm', 'mclogit', 'mlogit', 'mnlogit',
  'rms', 'relevent', 'sampleSelection', 'spdep', 'Zelig'
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'stars', 'nngeo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'lwgeom'

Packages suggested but not available for checking:
  'cubelyr', 'dplyr', 'exactextractr', 'ggforce', 'ggplot2',
  'ggthemes', 'ncdfgeom', 'ncmeta', 'starsdata', 'testthat', 'tidyr',
  'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 's2dverification'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'tibble', 'tidyr', 'patchwork', 'readr', 'car'

Packages suggested but not available for checking: 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'dbplyr', 'dm', 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'psycho', 'dplyr', 'Hmisc'

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: 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'pkgdown'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'statgenSTA'

Packages suggested but not available for checking: 'asreml', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'factoextra', 'ggforce', 'ggplot2', 'ggnewscale', 'SpATS'

Package suggested but not available for checking: 'asreml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'SpATS'

Packages suggested but not available for checking:
  'asreml', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tergm', 'ergm.count', 'sna', 'tsna', 'ergm', 'network',
  'networkDynamic'

Packages suggested but not available for checking:
  'ergm.rank', 'ergm.ego', 'EpiModel', 'degreenet', 'latentnet',
  'networksis', 'relevent', 'ndtv'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ergm', 'network', 'sna'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'tibble', 'tidyr', 'usethis'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tidytext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'readr'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat', 'tidyr', 'pkgdown', 'kableExtra',
  'leaflet', 'tmap', 'pct', 'osmdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ipmisc', 'tidyr'

Packages suggested but not available for checking:
  'afex', 'ggplot2', 'metaBMA', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'GGally', 'dplyr', 'ggdendro', 'tibble', 'ggfortify',
  'ggrepel', 'factoextra', 'pvca', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'lintr', 'pkgdown', 'rhub', 'roxygen2', 'testthat'
Running 'tests.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'broom.mixed', 'labelled', 'arm', 'tibble', 'dplyr',
  'forcats'

Package suggested but not available for checking: 'dbplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fda'

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: 'gh'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'readxl', 'rvest', 'sf', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'mapview', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'stm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'stm'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'stm', 'tidygraph', 'ggraph', 'ggrepel', 'ggplot2', 'dplyr',
  'tibble', 'readr'

Package suggested but not available for checking: 'quanteda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'fields'

Package suggested but not available for checking: 'demography'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dvmisc', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'lintr', 'quanteda', 'testthat'
Running 'lint.R'
Running the tests in 'tests/lint.R' failed.
Complete output:
  > library("lintr")
  Error in library("lintr") : there is no package called 'lintr'
  Execution halted
Package suggested but not available for checking: 'UsingR'
Packages required but not available: 'dplyr', 'lwgeom', 'sf'

Packages suggested but not available for checking:
  'testthat', 'dodgr', 'stats19', 'cyclestreets', 'leaflet', 'pct',
  'tmap', 'bench', 'osrm', 'mapsapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'shinyFiles', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'StrathE2E2examples', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > #
  > # A few long running tests make use of the testthat::skip_on_cran() mechanism so that they don't run when on CRAN
  > #
  > # This skip function relies on devtools package setting an environment variable NOT_CRAN, so if you want to run the tests
  > # locally you must either use devtools or set this variable explicitly yourself:
  > #
  > # cd StrathE2E2
  > # R
  > # > library(StrathE2E2)
  > # > Sys.setenv(NOT_CRAN="true")
  > # > testthat::test_dir("tests")
  > #
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespace in Imports field not imported from: 'bnlearn'
  All declared Imports should be used.
Packages required but not available: 'dplyr', 'ggplot2', 'ggparty'

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', 'StatMatch'
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'astrochron', 'RFOC', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'samr'
Namespace in Imports field not imported from: 'dbscan'
  All declared Imports should be used.
Package required but not available: 'ndjson'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'drc'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RcppParallel'

Packages suggested but not available for checking: 'qs', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  icu69/common/cstring.h:43:70: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 156 bytes from a string of length 156 [-Wstringop-truncation]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/stringi/stringi.Rcheck/00install.out' for details.
Packages required but not available:
  'ShortRead', 'tidyr', 'tibble', 'dplyr'

Package suggested but not available for checking: 'STRaitRazoR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spatialreg', 'dplyr', 'tidyr', 'testthat'

Packages suggested but not available for checking:
  'splm', 'spdep', 'sf', 'Ecdat', 'tidycensus', 'ggplot2', 'patchwork',
  'gt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'car', 'ggplot2', 'lmerTest', 'pbkrtest', 'phia'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'forecast'

Packages suggested but not available for checking:
  'testthat', 'demography', 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'car', 'dynlm'
Packages suggested but not available for checking: 'car', 'dynlm', 'bfast'
Package unavailable to check Rd xrefs: 'bfast'
Error(s) in re-building vignettes:
--- re-building 'StructFDR.Rmd' using rmarkdown
Loading required package: StructFDR
Loading required package: nlme
Loading required package: ape
Loading required package: cluster
Loading required package: dirmult
Loading required package: matrixStats
Loading required package: ggplot2
Loading required package: reshape
Quitting from lines 172-187 (StructFDR.Rmd) 
Error: processing vignette 'StructFDR.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building 'StructFDR.Rmd'

SUMMARY: processing the following file failed:
  'StructFDR.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'MplusAutomation'
Packages required but not available:
  'readr', 'tidyr', 'dplyr', 'tibble', 'skimr', 'visdat', '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:
  'caret', 'tidyverse', 'CCA', 'dplyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'rematch2', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'stylest-vignette.Rmd' using rmarkdown
Quitting from lines 22-23 (stylest-vignette.Rmd) 
Error: processing vignette 'stylest-vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'stylest-vignette.Rmd'

SUMMARY: processing the following file failed:
  'stylest-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'UpSetR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'siar'

Package suggested but not available for checking: 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'colourpicker', 'dplyr', 'randomForestSRC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GSVA', 'rvest', 'ChemmineR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', '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', 'ggplot2', 'readr', 'tidyr', 'ggrepel',
  'patchwork', 'forcats', 'naniar'

Package suggested but not available for checking: 'haven'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'lwgeom', 'rmapshaper', 'sf', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'pkgdown', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'plotly', 'readr', 'testthat', 'tidyr', 'tsibble', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'forcats', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'spdep', 'ggplot2', 'viridis', 'shadowtext', 'ggridges'

Packages suggested but not available for checking:
  'INLA', 'patchwork', 'rdhs', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'd3r', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'tidyr'

Package which this enhances but not available for checking: 'treemap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'dplyr', 'cartogram', 'rmapshaper', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'supc.Rmd' using rmarkdown
--- finished re-building 'supc.Rmd'

--- re-building 'supc_demo.Rmd' using rmarkdown
Quitting from lines 133-135 (supc_demo.Rmd) 
Error: processing vignette 'supc_demo.Rmd' failed with diagnostics:
there is no package called 'fields'
--- failed re-building 'supc_demo.Rmd'

SUMMARY: processing the following file failed:
  'supc_demo.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'referenceIntervals'

Packages suggested but not available for checking:
  'car', 'emojifont', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(SuperGauss)
  
  Attaching package: 'SuperGauss'
  
  The following object is masked from 'package:base':
  
      %*%
  
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'ggdendro'

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:
  'arm', 'caret', 'devtools', 'ggplot2', 'sva', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'Guide-to-SuperLearner.Rmd' using rmarkdown
Quitting from lines 191-213 (Guide-to-SuperLearner.Rmd) 
Error: processing vignette 'Guide-to-SuperLearner.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Guide-to-SuperLearner.Rmd'

SUMMARY: processing the following file failed:
  'Guide-to-SuperLearner.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'ClusterR', 'caret'
Running examples in 'superml-Ex.R' failed
The error most likely occurred in:

> ### Name: GridSearchCV
> ### Title: Grid Search CV
> ### Aliases: GridSearchCV
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `GridSearchCV$new`
> ## ------------------------------------------------
> 
> rf <- RFTrainer$new()
> gst <-GridSearchCV$new(trainer = rf,
+                       parameters = list(n_estimators = c(100),
+                                         max_depth = c(5,2,10)),
+                                         n_folds = 3,
+                                         scoring = c('accuracy','auc'))
> 
> ## ------------------------------------------------
> ## Method `GridSearchCV$fit`
> ## ------------------------------------------------
> 
> rf <- RFTrainer$new()
> gst <-GridSearchCV$new(trainer = rf,
+                       parameters = list(n_estimators = c(100),
+                                         max_depth = c(5,2,10)),
+                                         n_folds = 3,
+                                         scoring = c('accuracy','auc'))
> data("iris")
> gst$fit(iris, "Species")
[1] "entering grid search"
[1] "In total, 3 models will be trained"
Error in loadNamespace(x) : there is no package called 'caret'
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'test_miscs.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'tibble', 'cli', 'pillar'

Packages suggested but not available for checking:
  'car', 'lintr', 'testthat', 'vdiffr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'R.matlab' 'fBasics' 'spls'
  All declared Imports should be used.
Package required but not available: 'ClusterR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'afex', 'ggplot2', 'dplyr', 'Hmisc', '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: 'rcrossref'

Packages suggested but not available for checking: 'testthat', 'fulltext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'mlogit', 'gmnl', 'apollo'
Packages unavailable to check Rd xrefs: 'mlogit', 'gmnl', 'apollo'
Namespaces in Imports field not imported from:
  'doParallel' 'pROC'
  All declared Imports should be used.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'rms', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # load library
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Namespace in Imports field not imported from: 'learnr'
  All declared Imports should be used.
Packages required but not available: 'logistf', 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'plyr'
  All declared Imports should be used.
Package required but not available: 'SurvCorr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'survAUC-Ex.R' failed
The error most likely occurred in:

> ### Name: schemper
> ### Title: Distance-based estimator of survival predictive accuracy
> ###   proposed by Schemper and Henderson
> ### Aliases: schemper
> ### Keywords: classif
> 
> ### ** Examples
> 
> 
> library(rms)
Error in library(rms) : there is no package called 'rms'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'survCurve.Rmd' using rmarkdown
Quitting from lines 26-29 (survCurve.Rmd) 
Error: processing vignette 'survCurve.Rmd' failed with diagnostics:
there is no package called 'mstate'
--- failed re-building 'survCurve.Rmd'

SUMMARY: processing the following file failed:
  'survCurve.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'spdep', 'INLA'

Package which this enhances but not available for checking: 'ggplot2'
Packages unavailable to check Rd xrefs: 'spdep', 'ggplot2'
Running '3stage2phase.R'
  Running 'DBIcheck.R'
  Running 'api.R'
  Running 'badcal.R'
  Comparing 'badcal.Rout' to 'badcal.Rout.save' ... OK
  Running 'bycovmat.R'
  Running 'caleg.R'
  Running 'check.R'
  Comparing 'check.Rout' to 'check.Rout.save' ... OK
  Running 'contrast-replicates.R'
  Running 'coxph-termtest.R'
  Running 'deff.R'
  Comparing 'deff.Rout' to 'deff.Rout.save' ... OK
  Running 'defftest.R'
  Running 'domain.R'
  Comparing 'domain.Rout' to 'domain.Rout.save' ... OK
  Running 'fpc.R'
  Running 'glm-scoping.R'
  Running 'kalton.R'
  Comparing 'kalton.Rout' to 'kalton.Rout.save' ... OK
  Running 'logranktest.R'
  Running 'lonely.psu.R'
  Comparing 'lonely.psu.Rout' to 'lonely.psu.Rout.save' ... OK
  Running 'multistage.R'
  Running 'na_action.R'
  Running 'newquantile.R'
  Running 'nwts-cch.R'
  Running 'nwts.R'
  Comparing 'nwts.Rout' to 'nwts.Rout.save' ... OK
  Running 'poisson.R'
  Running 'pps.R'
  Running 'quantile.R'
  Comparing 'quantile.Rout' to 'quantile.Rout.save' ... OK
  Running 'quantiles-chile.R'
  Running 'rakecheck.R'
  Comparing 'rakecheck.Rout' to 'rakecheck.Rout.save' ... OK
  Running 'raowuboot.R'
  Comparing 'raowuboot.Rout' to 'raowuboot.Rout.save' ... OK
  Running 'regpredict.R'
  Comparing 'regpredict.Rout' to 'regpredict.Rout.save' ... OK
  Running 'scoping.R'
  Running 'survcurve.R'
  Comparing 'survcurve.Rout' to 'survcurve.Rout.save' ... OK
  Running 'svyby_se.R'
  Running 'svyivreg.R'
Running the tests in 'tests/svyivreg.R' failed.
Complete output:
  > library(survey)
  Loading required package: grid
  Loading required package: Matrix
  Loading required package: survival
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  > library(AER)
  Error in library(AER) : there is no package called 'AER'
  Execution halted
Packages required but not available:
  'flexsurv', 'dplyr', 'ggplot2', 'rms', 'rstan', 'tibble',
  'StanHeaders'

Packages suggested but not available for checking: 'shinystan', 'INLA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readr', 'tidyverse', 'factoextra', 'useful'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readr', 'tidyverse', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'tibble', 'tidyr', 'ggplot2', 'survminer',
  'cowplot', 'tidytidbits'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'pseudo', 'testthat'
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggpubr', 'broom', 'dplyr', 'tidyr', 'survMisc', 'tibble',
  'ggtext'

Packages suggested but not available for checking: 'flexsurv', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'broom', 'dplyr', 'forcats', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'survminer', 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test_survPen.r'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'ggsci'

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:
  'breakDown', 'ggplot2', 'pec', 'survminer'

Packages suggested but not available for checking:
  'DALEX', 'randomForestSRC', 'rms', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'L0Learn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'robets', 'forecastHybrid'

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', 'tsDyn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'caret'

Packages suggested but not available for checking: 'ggplot2', 'recipes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'fields', 'devtools'
Error(s) in re-building vignettes:
--- re-building 'swdft-intro.Rmd' using rmarkdown
Quitting from lines 211-212 (swdft-intro.Rmd) 
Error: processing vignette 'swdft-intro.Rmd' failed with diagnostics:
there is no package called 'fields'
--- failed re-building 'swdft-intro.Rmd'

SUMMARY: processing the following file failed:
  'swdft-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'broom', 'dplyr', 'forecast', 'tibble', 'tidyr', 'timetk'

Packages suggested but not available for checking:
  'forcats', 'testthat', 'readr', 'robets', 'tidyquant', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'swephRdata'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## inhibit overloading of ephemeris provided by
  > ## swephR and swephRdata
  > Sys.setenv(SE_EPHE_PATH = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'readr', 'swfscDAS', 'swfscMisc', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'sf', 'swfscMisc', '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', 'ggrepel', 'tibble', 'sf', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'rvest', '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: 'Hmisc', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'swirl', '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', 'tidyr', 'ggplot2', 'sf', 'tibble'

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:
  'ggplot2', 'sf', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'SWMPr', 'broom', 'dplyr', 'EnvStats', 'ggplot2', 'ggthemes',
  'leaflet', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'oce', 'dplyr', 'openair', 'tidyr'

Package suggested but not available for checking: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'sylly.de', 'sylly.es'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ./tests
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'RSDA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'symengine-Ex.R' failed
The error most likely occurred in:

> ### Name: D,SymEngineDataType-method
> ### Title: Derivatives of a Symbolic Expression
> ### Aliases: D,SymEngineDataType-method
> 
> ### ** Examples
> 
> expr <- S(~ exp(x))
> D(expr) == expr
[1] TRUE
> expr <- S(~ x^2 + 2*x + 1)
> D(expr)
Error(s) in re-building vignettes:
--- re-building 'odesystem.Rmd' using rmarkdown
Package suggested but not available for checking: 'mpoly'
Packages required but not available: 'OpenMx', 'metaSEM'

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', 'sf', 'rnaturalearth', 'metR', 'RNCEP', 'tidyr',
  'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'haven', 'testthat'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(data.table)
  > library(acs)
  Loading required package: stringr
  Loading required package: XML
  
  Attaching package: 'acs'
  
  The following object is masked from 'package:base':
  
      apply
  
  > library(synthACS)
  
  Attaching package: 'synthACS'
  
  The following object is masked from 'package:base':
  
      split
  
  > 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', 'ChainLadder'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'synthpop', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'unix', 'testthat'
Package required but not available: 'car'

Package suggested but not available for checking: 'sem'

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:
  'devtools', 'readxl', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'table1-examples.Rmd' using rmarkdown

Attaching package: 'table1'

The following objects are masked from 'package:base':

    units, units<-

--- finished re-building 'table1-examples.Rmd'

--- re-building 'table1-latex.Rmd' using rmarkdown
Quitting from lines 34-59 (table1-latex.Rmd) 
Error: processing vignette 'table1-latex.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'table1-latex.Rmd'

SUMMARY: processing the following file failed:
  'table1-latex.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'tibble', 'gt'
Error(s) in re-building vignettes:
--- re-building 'default_rounder.Rmd' using rmarkdown
--- finished re-building 'default_rounder.Rmd'

--- re-building 'table_guide.Rmd' using rmarkdown
Quitting from lines 19-25 (table_guide.Rmd) 
Error: processing vignette 'table_guide.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'table_guide.Rmd'

SUMMARY: processing the following file failed:
  'table_guide.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'labelled'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'geepack', 'lmerTest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'echarts4r'
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'ggtext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'kableExtra', 'Hmisc'
Packages unavailable to check Rd xrefs: 'Hmisc', 'kableExtra'
Packages required but not available:
  'dplyr', 'tidyr', 'kableExtra', 'spork'

Packages suggested but not available for checking:
  'yamlet', 'testthat', 'shinyFiles', 'haven'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'torch', 'hardhat', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'recipes', 'parsnip', 'dials', 'vip', 'tidyverse',
  'ggplot2', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'tidyr', 'testthat'

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', 'silicate', '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: 'dimensio', '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: 'ggforce', 'ggplot2'

Packages suggested but not available for checking: 'zipangu', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'tabulog.Rmd' using rmarkdown
Quitting from lines 13-17 (tabulog.Rmd) 
Error: processing vignette 'tabulog.Rmd' failed with diagnostics:
there is no package called 'readr'
--- failed re-building 'tabulog.Rmd'

SUMMARY: processing the following file failed:
  'tabulog.Rmd'

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: 'forecast'
Error(s) in re-building vignettes:
--- re-building 'new-high-level-functions.Rmd' using rmarkdown
--- finished re-building 'new-high-level-functions.Rmd'

--- re-building 'new-methods.Rmd' using rmarkdown
Quitting from lines 100-103 (new-methods.Rmd) 
Error: processing vignette 'new-methods.Rmd' failed with diagnostics:
there is no package called 'forecast'
--- failed re-building 'new-methods.Rmd'

--- re-building 'new-panel-functions.Rmd' using rmarkdown
--- finished re-building 'new-panel-functions.Rmd'

--- re-building 'tactile-theme.Rmd' using rmarkdown
--- finished re-building 'tactile-theme.Rmd'

SUMMARY: processing the following file failed:
  'new-methods.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'SpatialExtremes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'tidyverse', 'ggplot2'
Package suggested but not available for checking: 'miceadds'

Package which this enhances but not available for checking: 'LSAmitR'
Package unavailable to check Rd xrefs: 'miceadds'
Namespace in Imports field not imported from: 'jiebaR'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'testthat', 'rms', 'Hmisc', 'dplyr'
Packages required but not available: 'targets', 'tibble'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.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: 'cli', 'tibble'

Packages suggested but not available for checking:
  'dplyr', 'gt', 'pkgload', 'qs', 'testthat', 'torch', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'leaflet', 'sf', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Package suggested but not available for checking: 'tashudata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'shadowtext', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'patternplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'kableExtra'
Running examples in 'tatoo-Ex.R' failed
The error most likely occurred in:

> ### Name: as_latex
> ### Title: Convert a Table to Latex Code
> ### Aliases: as_latex save_pdf view_pdf
> 
> ### ** Examples
> 
>   as_latex(iris)
Error in loadNamespace(x) : there is no package called 'kableExtra'
Calls: as_latex ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package unavailable to check Rd xrefs: 'GEOmap'
Package required but not available: 'tibble'

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: 'dplyr', 'tibble', 'readr', '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', 'tibble', 'tidyr', 'pillar', 'cli'

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: 'GA', 'testthat'
Packages required but not available: 'dplyr', 'tibble', 'readr', 'dbplyr'

Packages suggested but not available for checking: 'testthat', 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'bold', 'ritis', 'worrms', 'natserv', 'wikitaxa', 'cli'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'taxa', 'taxize'

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: 'taxize', 'wikitaxa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'tboot.Rmd' using rmarkdown
Quitting from lines 105-112 (tboot.Rmd) 
Error: processing vignette 'tboot.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'tboot.Rmd'

--- re-building 'tboot_bmr.Rmd' using rmarkdown
Quitting from lines 66-83 (tboot_bmr.Rmd) 
Error: processing vignette 'tboot_bmr.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'tboot_bmr.Rmd'

SUMMARY: processing the following files failed:
  'tboot.Rmd' 'tboot_bmr.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggalt', 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Matrix' 'quadprog'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'viridis'
Error(s) in re-building vignettes:
--- re-building 'tcensReg.Rmd' using rmarkdown
Quitting from lines 63-76 (tcensReg.Rmd) 
Error: processing vignette 'tcensReg.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'tcensReg.Rmd'

SUMMARY: processing the following file failed:
  'tcensReg.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'cowplot'

Packages suggested but not available for checking: 'tcgsaseq', 'GEOquery'

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', 'mrgsolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'plotly', 'ggpubr', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'colorspace' 'psych'
  All declared Imports should be used.
Packages required but not available: 'Mcomp', 'forecast'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stringi'
  All declared Imports should be used.
Packages required but not available: 'TDAstats', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
Packages required but not available: 'SPOT', 'adabag'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', 'GA', 'sonicscrewdriver'
Packages required but not available: 'dplyr', 'devtools', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'DiagrammeR', 'leaflet', 'plotly', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'Lahman', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'httr' 'jsonlite'
  All declared Imports should be used.
Packages required but not available:
  'cowplot', 'dplyr', 'fields', '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', 'sf', 'tidyr'

Packages suggested but not available for checking: 'stars', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'arulesViz', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > # These tests are more extensive and only need to run on travis, not on CRAN.
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr', 'plotly'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'tfestimators'
Package unavailable to check Rd xrefs: 'tfestimators'
Packages required but not available: 'ergm', 'tergm', 'network', 'tibble'

Packages suggested but not available for checking: 'testthat', 'EpiModel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ergm', 'network', 'networkDynamic'

Packages suggested but not available for checking: 'tibble', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'colourpicker', 'readxl', 'testthat', 'vdiffr'
Packages required but not available: 'sf', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'intro.Rmd' using rmarkdown
Quitting from lines 18-22 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'intro.Rmd'

SUMMARY: processing the following file failed:
  'intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GIAValidationExample.Rmd' using rmarkdown
Quitting from lines 29-51 (GIAValidationExample.Rmd) 
Error: processing vignette 'GIAValidationExample.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'GIAValidationExample.Rmd'

SUMMARY: processing the following file failed:
  'GIAValidationExample.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'forcats'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'gurobi', 'kableExtra', 'testthat', 'pkgdown', 'pkgload'
Error(s) in re-building vignettes:
--- re-building 'constraints.Rmd' using rmarkdown
Quitting from lines 20-28 (constraints.Rmd) 
Error: processing vignette 'constraints.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'constraints.Rmd'

--- re-building 'rsymphony.Rmd' using rmarkdown
--- finished re-building 'rsymphony.Rmd'

SUMMARY: processing the following file failed:
  'constraints.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'caret', 'cutpointr', 'dplyr', '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:
  'fda', 'ggplot2', 'dplyr', 'ggpubr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'pkgload', 'waldo'

Packages suggested but not available for checking: 'mockery', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'pkgload', 'testthat', 'usethis'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'FactoMineR', 'tibble', 'ggrepel', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'devtools', 'readr', 'testthat'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'rematch2'

Packages suggested but not available for checking: 'kableExtra', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'broom', 'ggplot2', 'testthat'

Packages which this enhances but not available for checking:
  'AER', 'brms', 'btergm', 'dynlm', 'feisr', 'forecast', 'miceadds',
  'mlogit', 'mnlogit', 'Zelig'
Packages unavailable to check Rd xrefs: 'broom', 'Zelig', 'brms', 'btergm', 'dynlm', 'ergm', 'latentnet', 'forecast', 'feisr', 'geepack', 'miceadds', 'AER', 'sna', 'rms', 'erer', 'mlogit', 'mnlogit', 'panelAR', 'relevent', 'spatialreg', 'sampleSelection', 'tergm', 'systemfit', 'metaSEM', 'ggplot2'
Packages required but not available:
  'dplyr', 'googleAuthR', 'googleLanguageR'

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', 'tidytext', 'dplyr', 'ggplot2', 'forcats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'tibble', 'tidyr', 'tidytext'
Packages required but not available:
  'syuzhet', 'dplyr', 'tidyr', 'tidytext', 'tibble', 'ggplot2',
  'ggwordcloud'

Packages suggested but not available for checking:
  'readxl', 'ggrepel', 'ggpubr', 'ggraph', 'corrr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'qgraph', 'ggplot2', 'ggraph', 'ggforce', 'concaveman'
Package suggested but not available for checking: 'textreuse'
Package unavailable to check Rd xrefs: 'textreuse'
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'ggplot2', 'ggrepel', 'cowplot',
  'parsnip', 'recipes', 'rsample', 'tune', 'workflows', 'yardstick'

Packages suggested but not available for checking: 'testthat', 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'recipes', 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'janitor', 'testthat', 'textfeatures'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'textreadr'
Packages required but not available:
  'dplyr', 'lexicon', 'quanteda', 'textclean'

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', 'rsample', 'dplyr', 'tfestimators'
Packages required but not available: 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'modelr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'tfestimators', 'recipes', 'tibble'
Namespace in Imports field not imported from: 'ggm'
  All declared Imports should be used.
Package suggested but not available for checking: 'gdalcubes'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'gganimate', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'plotly', 'rstan', 'stm'

Packages suggested but not available for checking: 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'recipes', 'dplyr', 'tibble', 'unbalanced'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'Thermimage-Ex.R' failed
The error most likely occurred in:

> ### Name: diffFrame
> ### Title: A frame difference function for subtracting adjacent frames from
> ###   an imported thermal image sequence.
> ### Aliases: diffFrame
> 
> ### ** Examples
> 
> 
> # set w to 640 and h to 480
> w<-640
> h<-480
> f<-system.file("extdata", "SampleSEQ.seq", package = "Thermimage")
> x<-frameLocates(f)
> suppressWarnings(templookup<-raw2temp(1:65535))
> alldata<-unlist(lapply(x$f.start, getFrames, vidfile=f, w=w, h=h))
> alldata<-matrix(alldata, nrow=w*h, byrow=FALSE)
> alltemperature<-templookup[alldata]
> alltemperature<-unname(matrix(alltemperature, nrow=w*h, byrow=FALSE))
> 
> dalltemperature<-as.matrix(diffFrame(alltemperature, absolute=TRUE), nrow=w)
> 
> # Plot 
> plotTherm(dalltemperature[,1], templookup=NULL, w=w, h=h,  minrangeset=min(dalltemperature),
+           maxrangeset=max(dalltemperature), trans="mirror.matrix")
Error in loadNamespace(x) : there is no package called 'fields'
Calls: plotTherm ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'forecast', 'hts', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'dplyr', 'ggplot2', 'readr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'testthat'
Package required but not available: 'dipsaus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readxl', 'readr', 'janitor', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggrepel', 'fixerapi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'revdbayes'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'rstantools', 'MplusAutomation', 'dplyr', 'tibble', 'tidyr',
  'StanHeaders'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pillar'

Packages suggested but not available for checking:
  'bench', 'cli', 'DiagrammeR', 'dplyr', 'ggplot2', 'nycflights13',
  'testthat', 'tidyr'

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:
  'broom', 'gapminder', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tidyr', 'ggplot2'
Packages required but not available:
  'ggdist', 'dplyr', 'tidyr', 'ggplot2', 'tibble', 'posterior'

Packages suggested but not available for checking:
  'testthat', 'forcats', 'vdiffr', 'rstan', 'rstantools', 'rstanarm',
  'broom', 'dotwhisker', 'bayesplot', 'modelr', 'brms', 'cowplot',
  'ggrepel', 'gganimate', 'pkgdown', 'distributional', 'transformr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'readr', 'tibble'

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', 'modelr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyr', 'tibble', 'dplyr', 'forcats'

Packages suggested but not available for checking:
  'broom', 'ggplot2', 'ggforce'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'sf', 'dplyr', 'tigris', 'rvest', 'tidyr', 'readr'

Packages suggested but not available for checking: 'ggplot2', 'srvyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'matahari'

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:
  'broom', 'dplyr', 'forcats', 'MBESS', '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', 'tibble'

Packages suggested but not available for checking: 'explore', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggrepel', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyr', 'dplyr', 'testthat'
Packages suggested but not available for checking:
  'nycflights13', 'tidyr', 'ggplot2', 'dplyr', 'bench', 'testthat'
Packages unavailable to check Rd xrefs: 'dplyr', 'tidyr', 'fastDummies', 'sjmisc'
Error(s) in re-building vignettes:
--- re-building 'benchmark.Rmd' using rmarkdown
Quitting from lines 22-60 (benchmark.Rmd) 
Error: processing vignette 'benchmark.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'benchmark.Rmd'

--- re-building 'chinese_tutorial.Rmd' using rmarkdown
Quitting from lines 23-42 (chinese_tutorial.Rmd) 
Error: processing vignette 'chinese_tutorial.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'chinese_tutorial.Rmd'

--- re-building 'english_tutorial.Rmd' using rmarkdown
--- finished re-building 'english_tutorial.Rmd'

--- re-building 'example1_intro.Rmd' using rmarkdown
--- finished re-building 'example1_intro.Rmd'

--- re-building 'example2_join.Rmd' using rmarkdown
Quitting from lines 18-24 (example2_join.Rmd) 
Error: processing vignette 'example2_join.Rmd' failed with diagnostics:
there is no package called 'nycflights13'
--- failed re-building 'example2_join.Rmd'

--- re-building 'example3_reshape.Rmd' using rmarkdown
Quitting from lines 18-20 (example3_reshape.Rmd) 
Error: processing vignette 'example3_reshape.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'example3_reshape.Rmd'

--- re-building 'example4_nest.Rmd' using rmarkdown
--- finished re-building 'example4_nest.Rmd'

--- re-building 'example5_fst.Rmd' using rmarkdown
--- finished re-building 'example5_fst.Rmd'

--- re-building 'example6_dt.Rmd' using rmarkdown
--- finished re-building 'example6_dt.Rmd'

SUMMARY: processing the following files failed:
  'benchmark.Rmd' 'chinese_tutorial.Rmd' 'example2_join.Rmd'
  'example3_reshape.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages unavailable to check Rd xrefs: 'dplyr', 'tidyr', 'fastDummies'
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
Quitting from lines 113-154 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'Introduction.Rmd'

SUMMARY: processing the following file failed:
  'Introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'tidyr', 'readxl', '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: 'tibble', 'dplyr', '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', 'tidyr', 'fuzzyjoin'

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'

Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyRSS', 'sf'

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: 'tibble', 'dplyr', 'tidyr', 'pillar'

Packages suggested but not available for checking: 'network', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'viridis', 'dendextend'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dbplyr', 'dplyr', 'readr', '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: 'dplyr', 'tidyr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'forcats', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr', 'tidytext'

Packages suggested but not available for checking: 'quanteda', '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:
  'testthat', 'forcats', 'bench'

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', 'tidytext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'MplusAutomation', 'tibble'

Packages suggested but not available for checking: 'pillar', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'ggrepel', 'car', 'cowplot', 'Evomorph', 'factoextra',
  'plotly', 'broom', 'dplyr', 'ggplot2', 'tibble', '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:
  'broom', 'cli', 'dials', 'dplyr', 'ggplot2', 'infer', 'parsnip',
  'recipes', 'rsample', 'tibble', 'tidyr', 'tune', 'workflows',
  'workflowsets', 'yardstick'

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:
  'tidyr', 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'ncmeta', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'cubelyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forcats', 'janitor', 'tibble', 'tidyr', 'vroom'

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', 'styler', 'ggstance', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'patchwork', 'forcats', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'readr'

Packages suggested but not available for checking:
  'europepmc', 'tidytext', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rsample', 'tidyr', 'dplyr', 'rstanarm', 'tibble', 'ggplot2', 'tune',
  'workflowsets'

Packages suggested but not available for checking:
  'testthat', 'parsnip', 'yardstick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'testthat', 'nycflights13', 'parsnip'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'riingo', 'readr', 'alphavantager', 'tibble',
  'tidyr', 'timetk', 'cli', 'janitor'

Packages suggested but not available for checking:
  'tidyverse', 'tibbletime', 'forcats', 'broom', 'testthat', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'dbplyr', 'dtplyr', 'nycflights13', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'labelled'

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', 'janitor', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'redcapAPI'

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:
  'readr', 'repurrrsive', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking: '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:
  'AmesHousing', 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'syntax.Rmd' using rmarkdown
Quitting from lines 27-33 (syntax.Rmd) 
Error: processing vignette 'syntax.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'syntax.Rmd'

--- re-building 'tidyselect.Rmd' using rmarkdown
Quitting from lines 23-31 (tidyselect.Rmd) 
Error: processing vignette 'tidyselect.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'tidyselect.Rmd'

SUMMARY: processing the following files failed:
  'syntax.Rmd' 'tidyselect.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'OpenMx', 'MplusAutomation'

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:
  'Seurat', 'tibble', 'dplyr', 'tidyr', 'ggplot2', 'plotly', 'pillar',
  'cli'

Packages suggested but not available for checking:
  'testthat', 'GGally', 'SingleR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dplyr', 'pillar', 'tibble', 'testthat'

Packages suggested but not available for checking: 'bioseq', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'readr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'lmerTest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'dplyr', 'ggplot2', 'tidyr', 'forcats'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'readr', 'tidyr', 'quanteda', 'ggplot2', 'testthat', 'vdiffr', 'stm',
  'broom', 'textdata'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'forcats', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'readr', 'sf', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidybayes', 'tidyr', 'dplyr', 'readr'

Packages suggested but not available for checking: 'ggplot2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'ggtree', 'testthat', 'treeio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'readxl', 'rvest', 'readr', 'usethis'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'fuzzyjoin', 'ggplot2', 'sf', 'tigris'

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', 'cli', 'dbplyr', 'dplyr', 'dtplyr', 'forcats',
  'googledrive', 'googlesheets4', 'ggplot2', 'haven', 'modelr',
  'pillar', 'readr', 'readxl', 'reprex', 'rvest', 'tibble', 'tidyr'

Packages suggested but not available for checking: 'feather', '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: 'vpc', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'WikidataR', 'tibble', 'usethis',
  'WikidataQueryServiceR'

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', 'readxl', 'dplyr', 'tidyr', 'tibble', 'ggplot2',
  'cellranger'
Error(s) in re-building vignettes:
--- re-building 'data-validation-rules.Rmd' using rmarkdown
Quitting from lines 34-39 (data-validation-rules.Rmd) 
Error: processing vignette 'data-validation-rules.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'data-validation-rules.Rmd'

--- re-building 'smells.Rmd' using rmarkdown
Quitting from lines 60-71 (smells.Rmd) 
Error: processing vignette 'smells.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'smells.Rmd'

--- re-building 'tidyxl.Rmd' using rmarkdown
Quitting from lines 73-75 (tidyxl.Rmd) 
Error: processing vignette 'tidyxl.Rmd' failed with diagnostics:
there is no package called 'readxl'
--- failed re-building 'tidyxl.Rmd'

SUMMARY: processing the following files failed:
  'data-validation-rules.Rmd' 'smells.Rmd' 'tidyxl.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  read.c:19:5: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  read.c:20:5: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  read.c:260:2: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  read.c:261:2: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  read.c:262:2: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  read.c:263:2: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  read.c:266:2: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  read.c:301:6: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  read.c:317:3: warning: 'uint16' is deprecated [-Wdeprecated-declarations]
  read.c:318:3: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  read.c:561:4: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  read.c:581:4: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  write.c:36:5: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  write.c:130:7: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  write.c:180:6: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
  write.c:186:6: warning: 'uint32' is deprecated [-Wdeprecated-declarations]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/tiff/tiff.Rcheck/00install.out' for details.
Packages required but not available: 'abd', 'mosaic', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggthemes', 'leaflet', 'tidycensus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/tiledb/tiledb.Rcheck/00install.out' for details.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'lwgeom', 'sf', 'smoothr'

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', 'leaflet'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > source("./testthat/utils.R")
  > 
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)
  +   test_check("timechange")
  + }
  Error in packageVersion("testthat") : 
    there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'mtconnectR'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'TimeProjection-Ex.R' failed
The error most likely occurred in:

> ### Name: plotCalendarHeatmap
> ### Title: Calendar Heatmap
> ### Aliases: plotCalendarHeatmap
> 
> ### ** Examples
> 
> dates = timeSequence(from = '2012-01-01', to = '2012-12-31', by = 'day')
>    plotCalendarHeatmap(as.Date(dates), 1:366)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Loading required package: plyr
Error in ggplot(tp, aes(monthweek, weekday, fill = values)) : 
  could not find function "ggplot"
Calls: plotCalendarHeatmap
Execution halted
Package required but not available: 'pec'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'lubridate'
  All declared Imports should be used.
Package required but not available: 'forecast'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'recipes', 'rsample', 'dplyr', 'ggplot2', 'forcats', 'plotly',
  'padr', 'readr', 'tibble', 'tidyr', 'forecast'

Packages suggested but not available for checking:
  'tidyquant', 'tidymodels', 'modeltime', 'workflows', 'parsnip',
  'tune', 'yardstick', 'tidyverse', 'robets', 'broom', 'testthat',
  'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'tintHtmlIntro.Rmd' using rmarkdown
Quitting from lines 17-34 (tintHtmlIntro.Rmd) 
Error: processing vignette 'tintHtmlIntro.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'tintHtmlIntro.Rmd'

--- re-building 'tintPdfIntro.Rmd' using rmarkdown
Quitting from lines 17-33 (tintPdfIntro.Rmd) 
Error: processing vignette 'tintPdfIntro.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'tintPdfIntro.Rmd'

SUMMARY: processing the following files failed:
  'tintHtmlIntro.Rmd' 'tintPdfIntro.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in 'tinylabels-Ex.R' failed
The error most likely occurred in:

> ### Name: label_variable
> ### Title: Label Variables Using Pipes
> ### Aliases: label_variable label_variables
> 
> ### ** Examples
> 
>   library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'tinylabels_vignette.Rmd' using rmarkdown
Quitting from lines 131-134 (tinylabels_vignette.Rmd) 
Error: processing vignette 'tinylabels_vignette.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'tinylabels_vignette.Rmd'

SUMMARY: processing the following file failed:
  'tinylabels_vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'gt', 'rvest'

Package suggested but not available for checking: 'roxygen2'

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', 'broom', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'ggplot2'
Packages required but not available:
  'dplyr', 'ggplot2', 'cowplot', 'ggridges', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ReDaMoR', 'dplyr', 'RClickhouse', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tmaptools', 'sf', 'stars', 'leaflet', 'leafsync', 'leafem'

Packages suggested but not available for checking:
  'rmapshaper', 'cartogram', 'osmdata', 'ggplot2', 'dplyr', 'tidyr',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'lwgeom', 'stars'

Packages suggested but not available for checking:
  'tmap', 'rmapshaper', 'osmdata', 'OpenStreetMap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'tmod_gallery.Rmd' using rmarkdown
Quitting from lines 11-17 (tmod_gallery.Rmd) 
Error: processing vignette 'tmod_gallery.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'tmod_gallery.Rmd'

SUMMARY: processing the following file failed:
  'tmod_gallery.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ./testthat
  > 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > # tm is only imported
  > require(tm)
  Loading required package: tm
  Loading required package: NLP
  > test_check("tm.plugin.koRpus")
  Error in test_check("tm.plugin.koRpus") : 
    could not find function "test_check"
  Execution halted
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'testthat', 'tm.lexicon.GeneralInquirer'
Packages unavailable to check Rd xrefs: 'readtext', 'Rpoppler'
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'dexterMST'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'parsedate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'sf', 'tibble', 'readr'

Packages suggested but not available for checking:
  'ggplot2', 'cancensus', 'tidycensus', 'readxl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'stm'
Packages required but not available: 'qpgraph', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'torch'

Packages suggested but not available for checking: 'testthat', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'torch', 'torchvision'

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: 'quanteda'

Packages suggested but not available for checking:
  'toscaData', 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'bibliometrix', 'CINNA', 'dplyr', 'tidyr', 'tibble'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'engsoccerdata'
Running examples in 'TouRnament-Ex.R' failed
The error most likely occurred in:

> ### Name: leaguetable
> ### Title: Create a league table
> ### Aliases: leaguetable
> 
> ### ** Examples
> 
> #league table for La Liga 94/95 with three point rewards (instead of two) and home and away results
> require(engsoccerdata)
Loading required package: engsoccerdata
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'engsoccerdata'
> leaguetable(dataset=engsoccerdata::spain[which(engsoccerdata::spain$Season==1994),],
+ home="home", away="visitor",score_home="hgoal", score_away="vgoal", date="Date",
+ points = c(3,1,0), rank_by = c("Pts_DC","GD_DC","GF_DC","GD","GF"), DC_display = TRUE)
Error in loadNamespace(x) : there is no package called 'engsoccerdata'
Calls: leaguetable ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'leaflet', 'ggplot2', '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: 'MESS'

Package suggested but not available for checking: 'geepack'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tibble', 'forcats'

Packages suggested but not available for checking:
  'testthat', 'haven', 'tidyverse', 'readr', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'readxl', 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'tracerer-Ex.R' failed
The error most likely occurred in:

> ### Name: is_posterior
> ### Title: Determines if the input is a BEAST2 posterior
> ### Aliases: is_posterior
> 
> ### ** Examples
> 
> trees_filename <- get_tracerer_path("beast2_example_output.trees")
> tracelog_filename <- get_tracerer_path("beast2_example_output.log")
> posterior <- parse_beast_posterior(
+   trees_filename = trees_filename,
+   tracelog_filename = tracelog_filename
+ )
Error in loadNamespace(x) : there is no package called 'testthat'
Calls: parse_beast_posterior ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'demo.Rmd' using rmarkdown
Quitting from lines 76-82 (demo.Rmd) 
Error: processing vignette 'demo.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'demo.Rmd'

SUMMARY: processing the following file failed:
  'demo.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'readr', 'dplyr', 'ggplot2', 'moveVis', 'moveHMM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'trackeR', 'plotly', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'ggridges', 'fda', 'leaflet', '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', 'Momocs', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tibble', 'ggplot2', 'dplyr', 'tidyr', 'cli', 'broom'

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: 'competitiontoolbox'
Package unavailable to check Rd xrefs: 'competitiontoolbox'
Packages required but not available: 'caret', 'dplyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'adabag', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble', 'tidyr', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble', 'tidyr'
Running examples in 'traipse-Ex.R' failed
The error most likely occurred in:

> ### Name: track_query
> ### Title: Query track data for arbitrary locations
> ### Aliases: track_query
> 
> ### ** Examples
> 
> track_query(trips0$x[1:10], trips0$y[1:10], query = c(4.5, 5.5, 6.5))
Warning in track_query(trips0$x[1:10], trips0$y[1:10], query = c(4.5, 5.5,  :
  date is null, so assuming linear relative movement in time
Error in loadNamespace(x) : there is no package called 'tibble'
Calls: track_query ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'tibble', 'readr', 'taxize', 'rvest'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'TrajDataMining-Ex.R' failed
The error most likely occurred in:

> ### Name: owMeratniaByCollection
> ### Title: Ow Meratnial By Collection
> ### Aliases: owMeratniaByCollection
> ###   owMeratniaByCollection,TracksCollection,numeric,numeric-method
> 
> ### ** Examples
> 
> 
> library(magrittr)
> 
> library(sp)
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'TrajDataMining.Rmd' using rmarkdown
Quitting from lines 36-42 (TrajDataMining.Rmd) 
Error: processing vignette 'TrajDataMining.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'TrajDataMining.Rmd'

SUMMARY: processing the following file failed:
  'TrajDataMining.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'OpenStreetMap', 'forecast', 'taxidata'
Running examples in 'trajectories-Ex.R' failed
The error most likely occurred in:

> ### Name: auto.arima.Track
> ### Title: Fitting arima model to a track
> ### Aliases: auto.arima.Track
> 
> ### ** Examples
> 
> X <- rTrack()
> auto.arima.Track(X)
Error in auto.arima.Track(X) : 
  package forecast required, please install it first
Execution halted
Error(s) in re-building vignettes:
--- re-building 'article.Rnw' using Sweave

Error: processing vignette 'article.Rnw' failed with diagnostics:
 chunk 14 
Error in library("forecast") : there is no package called 'forecast'

--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
  'article.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'Hmisc'

Package suggested but not available for checking: 'TraMineRextras'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'tramME.Rnw' using knitr
Loading required package: tram
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Quitting from lines 62-119 (tramME.Rnw) 
Error: processing vignette 'tramME.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'tramME.Rnw'

SUMMARY: processing the following file failed:
  'tramME.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'mlrMBO', 'mlr', 'smoof'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'mlt.docreg', 'asht'
Packages required but not available: 'ggformula', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'transplantr-Ex.R' failed
The error most likely occurred in:

> ### Name: epts
> ### Title: Estimated Post-Transplant Survival Score (EPTS)
> ### Aliases: epts
> 
> ### ** Examples
> 
> epts(age = 23.5838467, dm = 0, prev_tx = 1, dx = 5.0814511)
Error: The dplyr package is needed for this function to work. Please install it.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'egfr.Rmd' using rmarkdown
Quitting from lines 32-34 (egfr.Rmd) 
Error: processing vignette 'egfr.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'egfr.Rmd'

--- re-building 'hla_mismatch_grade.Rmd' using rmarkdown
Quitting from lines 31-34 (hla_mismatch_grade.Rmd) 
Error: processing vignette 'hla_mismatch_grade.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'hla_mismatch_grade.Rmd'

--- re-building 'kidney_risk_scores.Rmd' using rmarkdown
Quitting from lines 37-39 (kidney_risk_scores.Rmd) 
Error: processing vignette 'kidney_risk_scores.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'kidney_risk_scores.Rmd'

--- re-building 'liver_recipient_scoring.Rmd' using rmarkdown
Quitting from lines 34-36 (liver_recipient_scoring.Rmd) 
Error: processing vignette 'liver_recipient_scoring.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'liver_recipient_scoring.Rmd'

SUMMARY: processing the following files failed:
  'egfr.Rmd' 'hla_mismatch_grade.Rmd' 'kidney_risk_scores.Rmd'
  'liver_recipient_scoring.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'cli', 'testthat'
Running examples in 'transx-Ex.R' failed
The error most likely occurred in:

> ### Name: filter_hamilton
> ### Title: Hamilton Filter
> ### Aliases: filter_hamilton
> 
> ### ** Examples
> 
> unemp <- ggplot2::economics$unemploy
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'motivation.Rmd' using rmarkdown
Quitting from lines 34-36 (motivation.Rmd) 
Error: processing vignette 'motivation.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'motivation.Rmd'

SUMMARY: processing the following file failed:
  'motivation.Rmd'

Error: Vignette re-building failed.
Execution halted
Errors in running code in vignettes:
when running code in 'trapezoid.Rnw'

> options(width = 70)

> options(continue = " ")

> require(trapezoid)
Loading required package: trapezoid

> require(plyr)
Loading required package: plyr

> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'

> x <- seq(from = 0, to = 1, by = 0.01)

> density <- dtrapezoid(x, min = 0, mode1 = 1/3, mode2 = 2/3, 
+     max = 1, n1 = 2, n3 = 2, alpha = 1)

> trapezoid <- ggplot(data = data.frame(x, density), 
+     aes(x = x, y = density)) + geom_line() + theme_bw()

  When sourcing 'trapezoid.R':
Error: could not find function "ggplot"
Execution halted

  'trapezoid.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'trapezoid.Rnw' using Sweave
Loading required package: trapezoid
Loading required package: plyr
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'

Error: processing vignette 'trapezoid.Rnw' failed with diagnostics:
 chunk 2 (label = trapezoid) 
Error in ggplot(data = data.frame(x, density), aes(x = x, y = density)) : 
  could not find function "ggplot"

--- failed re-building 'trapezoid.Rnw'

SUMMARY: processing the following file failed:
  'trapezoid.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'tidyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'treecm.Rnw' using Sweave

Error: processing vignette 'treecm.Rnw' failed with diagnostics:
 chunk 14 (label = exStabilization5) 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'treecm.Rnw'

SUMMARY: processing the following file failed:
  'treecm.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'phyloseq', 'ggplot2'

Packages suggested but not available for checking:
  'adaptiveGPCA', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'kdensity', 'readxl', 'testthat', 'TreeDistData',
  'Umatrix', 'vdiffr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat", warn.conflicts = FALSE)
  Error in library("testthat", warn.conflicts = FALSE) : 
    there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggparty', 'ggplot2', 'dplyr', 'ggnewscale', 'tidyr', 'yardstick'

Packages suggested but not available for checking: 'forcats', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'adegenet', 'adephylo', 'fields', 'RLumShiny'

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: 'ggtree', 'ggplot2'
Error(s) in re-building vignettes:
--- re-building 'structuredCoalescent.Rmd' using rmarkdown
Quitting from lines 64-65 (structuredCoalescent.Rmd) 
Error: processing vignette 'structuredCoalescent.Rmd' failed with diagnostics:
"ggtree" %in% utils::installed.packages()[, 1] is not TRUE
--- failed re-building 'structuredCoalescent.Rmd'

SUMMARY: processing the following file failed:
  'structuredCoalescent.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'lidR', 'sf', 'stars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'autocogs', 'tidyr'

Packages suggested but not available for checking:
  'plotly', 'testthat', 'gapminder'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'trending', 'yardstick', 'rsample', 'tidyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'ciTools'

Packages suggested but not available for checking:
  'brms', 'ggplot2', 'patchwork', 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'Rssa', 'imputeTS'

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: 'gtrendsR', 'dplyr', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tibble', 'dplyr', 'sensitivity'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rstan', 'rstantools', 'dplyr', 'ggplot2', 'tidybayes', 'tibble',
  'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'ggridges', 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ggtern'

Packages suggested but not available for checking:
  'testthat', 'sf', 'leaflet', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'RcppParallel', 'rstan', 'rstantools', 'dplyr', 'tidyr', 'bayesplot',
  'StanHeaders'

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: 'sf', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'ez'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'DALEX', 'ggdendro', '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: 'viridis', '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', 'tibble', 'tidyr', 'haven'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'GA', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'hdrcde'

Packages suggested but not available for checking: 'dplyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'hdrcde'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'readr', 'ggplot2', 'forcats', 'ez'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'tseries'
  All declared Imports should be used.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'tibble', 'forecast', 'ggplot2', 'tsibble',
  'tsibbledata', 'tibbletime', 'nycflights13', 'imputeTS'
Running examples in 'tsbox-Ex.R' failed
The error most likely occurred in:

> ### Name: ts_ts
> ### Title: Convert Everything to Everything
> ### Aliases: ts_ts ts_data.frame ts_df ts_data.table ts_dt ts_tbl
> ###   ts_tibbletime ts_timeSeries ts_tis ts_irts ts_tsibble ts_tslist
> ###   ts_xts ts_zoo
> 
> ### ** Examples
> 
> 
> x.ts <- ts_c(mdeaths, fdeaths)
> head(x.ts)
     mdeaths fdeaths
[1,]    2134     901
[2,]    1863     689
[3,]    1877     827
[4,]    1877     677
[5,]    1492     522
[6,]    1249     406
> head(ts_df(x.ts))
       id       time value
1 mdeaths 1974-01-01  2134
2 mdeaths 1974-02-01  1863
3 mdeaths 1974-03-01  1877
4 mdeaths 1974-04-01  1877
5 mdeaths 1974-05-01  1492
6 mdeaths 1974-06-01  1249
> 
> suppressMessages(library(dplyr))
Error in library(dplyr) : there is no package called 'dplyr'
Calls: suppressMessages -> withCallingHandlers -> library
Execution halted
Packages required but not available: 'ICtest', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'TSclust'

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', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'tidyr', 'dplyr', 'Mcomp', 'GGally'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tsibble'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'nycflights13', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dendextend', 'dplyr', 'plotly', 'tsibble'

Packages suggested but not available for checking: 'fabletools', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'MAPA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'RcppParallel'

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: 'network', 'networkDynamic'

Packages suggested but not available for checking:
  'networkDynamicData', 'testthat', 'sna', 'relevent', 'ergm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'EMD', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'TSrepr_extentions.Rmd' using rmarkdown
Quitting from lines 26-41 (TSrepr_extentions.Rmd) 
Error: processing vignette 'TSrepr_extentions.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'TSrepr_extentions.Rmd'

--- re-building 'TSrepr_representations_of_time_series.Rmd' using rmarkdown
Quitting from lines 83-85 (TSrepr_representations_of_time_series.Rmd) 
Error: processing vignette 'TSrepr_representations_of_time_series.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'TSrepr_representations_of_time_series.Rmd'

--- re-building 'TSrepr_representations_use_case.Rmd' using rmarkdown
Quitting from lines 22-28 (TSrepr_representations_use_case.Rmd) 
Error: processing vignette 'TSrepr_representations_use_case.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'TSrepr_representations_use_case.Rmd'

SUMMARY: processing the following files failed:
  'TSrepr_extentions.Rmd' 'TSrepr_representations_of_time_series.Rmd'
  'TSrepr_representations_use_case.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'dsa'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'bfast', 'broom', 'ggplot2'

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'forecast', 'forecastHybrid', 'plotly', 'tidyr', 'tsibble',
  'viridis'

Packages suggested but not available for checking: 'devtools', 'UKgrid'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'forecast', 'MAPA'

Package suggested but not available for checking: 'thief'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'TSVC-Ex.R' failed
The error most likely occurred in:

> ### Name: TSVC
> ### Title: Tree-Structured Modelling of Varying Coefficients
> ### Aliases: TSVC print.TSVC
> 
> ### ** Examples
> 
> # Swiss Labour Market 
> library(AER)
Error in library(AER) : there is no package called 'AER'
Execution halted
Packages required but not available:
  'dplyr', 'plotly', 'forecast', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'latticeExtra'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'example.Rmd' using rmarkdown
Quitting from lines 41-43 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'example.Rmd'

SUMMARY: processing the following file failed:
  'example.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'doBy'

Package suggested but not available for checking: 'pbkrtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'pbkrtest'

Package suggested but not available for checking: 'CorrBin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'klaR'
Packages required but not available: 'mlrMBO', 'mlr', 'smoof'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'cli', 'dials', 'dplyr', 'ggplot2', 'hardhat', 'parsnip', 'recipes',
  'rsample', 'tibble', 'tidyr', 'workflows', 'yardstick'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidyverse', 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggthemes', 'ggplot2', 'dplyr', 'tidyr', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 54-62 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'gapminder', 'dplyr', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'OVtool'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'onewaytests', 'ggplot2', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'forcats'

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:
  'haldensify', 'ggplot2', 'tibble', 'cli'

Package suggested but not available for checking: 'testthat'

Package which this enhances but not available for checking: 'sl3'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'waldo'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'exifr', 'link2GI'

Package suggested but not available for checking: 'mapview'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'PKNCA', 'readxl'

Packages suggested but not available for checking:
  'GA', 'GGally', 'testthat', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'DMwR2', 'ggplot2'
Running examples in 'UBL-Ex.R' failed
The error most likely occurred in:

> ### Name: ImbC
> ### Title: Synthetic Imbalanced Data Set for a Multi-class Task
> ### Aliases: ImbC
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 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'
> data(ImbC)
> summary(ImbC)
       X1              X2         Class    
 Min.   :-13.5843   cat :300   normal:859  
 1st Qu.: -2.6930   dog :400   rare1 : 10  
 Median : -0.1592   fish:300   rare2 :131  
 Mean   : -0.1064                          
 3rd Qu.:  2.4633                          
 Max.   : 12.7836                          
> ggplot(data=ImbC, aes(x=X2, y=X1, color=Class))+geom_jitter()
Error in ggplot(data = ImbC, aes(x = X2, y = X1, color = Class)) : 
  could not find function "ggplot"
Execution halted
Packages required but not available:
  'ggplot2', 'rstan', 'rstantools', 'StanHeaders'

Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ChemmineR', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dendextend'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ezcox', 'forcats', 'ggplot2', 'ggpubr', 'tibble', 'tidyr',
  'UCSCXenaTools'

Packages suggested but not available for checking:
  'cowplot', 'ggrepel', 'ggstatsplot', 'plotly', 'survminer',
  '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', 'ggplot2', 'ggrepel', 'ggridges', 'kableExtra'

Packages suggested but not available for checking:
  'car', 'GGally', 'MBESS', 'rio', 'viridis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'ukbabynames-Ex.R' failed
The error most likely occurred in:

> ### Name: ewbabynames
> ### Title: England & Wales baby names
> ### Aliases: ewbabynames
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  'dplyr', 'readr', 'ggplot2', 'tibble', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tsibble'

Packages suggested but not available for checking:
  'devtools', 'TSstudio', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tibble'

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr', 'leaflet', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'fields', 'AdaptGauss'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'OpenMx', 'ggplot2', 'cowplot', 'DiagrammeR', 'kableExtra'

Packages suggested but not available for checking:
  'devtools', 'hrbrthemes', 'Hmisc', 'testthat', 'rhub'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'mlr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'devtools', '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:
  'MortalityLaws', 'testthat'
Package unavailable to check Rd xrefs: 'MortalityLaws'
Packages required but not available:
  'dplyr', 'forcats', 'tidyr', 'readxl', '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', 'rstan'
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyverse', 'ggpubr', 'alakazam', 'gprofiler2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'vroom'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' calls not declared from:
  'unitizerdummypkg1' 'unitizerdummypkg2'
Packages suggested but not available for checking:
  'pillar', 'dplyr', 'testthat', 'ggforce'
Running 'plot.R'
  Running 'set_units.R'
Running the tests in 'tests/set_units.R' failed.
Complete output:
  > library(units)
  udunits database from C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/units/units.Rcheck/units/share/udunits/udunits2.xml
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'nlist', 'testthat'
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'gapminder', 'tidyr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'repurrrsive', 'roxygen2', 'testthat', 'tibble', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'tidyr.Rmd' using rmarkdown
Quitting from lines 32-37 (tidyr.Rmd) 
Error: processing vignette 'tidyr.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'tidyr.Rmd'

SUMMARY: processing the following file failed:
  'tidyr.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'forcats', 'tidyr', 'pillar', 'tibble', 'cellranger'

Packages suggested but not available for checking:
  'readr', 'readxl', 'rvest', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'unrtf-Ex.R' failed
The error most likely occurred in:

> ### Name: unrtf
> ### Title: Convert rtf Documents
> ### Aliases: unrtf
> 
> ### ** Examples
> 
> library(unrtf)
> text <- unrtf("https://jeroen.github.io/files/sample.rtf", format = "text")
No config directories. Searched: ../share/
Error: System call to 'unrtf' failed
Execution halted
Packages required but not available: 'tibble', 'tidyr', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'simstandard', 'ggplot2',
  'ggnormalviolin', 'patchwork'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'forcats', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'readxl', 'tidyr', 'devtools', 'ggplot2'
Running examples in 'unvotes-Ex.R' failed
The error most likely occurred in:

> ### Name: un_roll_calls
> ### Title: Data on each roll call of the United Nations General Assembly
> ### Aliases: un_roll_calls
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(dplyr)
Error in library(dplyr) : there is no package called 'dplyr'
Execution halted
Error(s) in re-building vignettes:
--- re-building 'unvotes.Rmd' using rmarkdown
Quitting from lines 26-30 (unvotes.Rmd) 
Error: processing vignette 'unvotes.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'unvotes.Rmd'

SUMMARY: processing the following file failed:
  'unvotes.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'colors.Rmd' using rmarkdown
--- finished re-building 'colors.Rmd'

--- re-building 'combinationModes.Rmd' using rmarkdown
Quitting from lines 20-22 (combinationModes.Rmd) 
Error: processing vignette 'combinationModes.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 'combinationModes.Rmd'

--- re-building 'got.Rmd' using rmarkdown
--- finished re-building 'got.Rmd'

--- re-building 'kmap.Rmd' using rmarkdown
--- finished re-building 'kmap.Rmd'

--- re-building 'upsetjs.Rmd' using rmarkdown
--- finished re-building 'upsetjs.Rmd'

--- re-building 'venn.Rmd' using rmarkdown
--- finished re-building 'venn.Rmd'

SUMMARY: processing the following file failed:
  'combinationModes.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'readxl', 'readr', 'ggplot2', 'dplyr', 'tidytext', 'textclean', 'sf',
  'tgamtheme'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Note that you would never run this file directly. This is used by tools::testInstallPackages()
  > # and other packages like covr.
  > # To actually run the tests, you need to set the working directory then run
  > # devtools::test('r-pkg/uptasticsearch')
  > 
  > # This line ensures that R CMD check can run tests.
  > # See https://github.com/hadley/testthat/issues/144
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(uptasticsearch)
  > 
  > testthat::test_check('uptasticsearch')
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages suggested but not available for checking:
  'sampleSelection', 'mlogit'
Error(s) in re-building vignettes:
--- re-building 'ExtendedAppendix.Rnw' using knitr
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'ExtendedAppendix.Rnw'

--- re-building 'Manuscript.Rnw' using knitr
Quitting from lines 159-160 (Manuscript.Rnw) 
Error: processing vignette 'Manuscript.Rnw' failed with diagnostics:
there is no package called 'sampleSelection'
--- failed re-building 'Manuscript.Rnw'

SUMMARY: processing the following file failed:
  'Manuscript.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'cli'

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'sf', 'IRdisplay', 'leaflet', 'leafem', 'leafpop'
Packages suggested but not available for checking:
  'sf', 'testthat', 'USAboundariesData', 'dplyr', 'leaflet'
Error(s) in re-building vignettes:
--- re-building 'usaboundaries-sample-analysis.Rmd' using rmarkdown
Quitting from lines 23-30 (usaboundaries-sample-analysis.Rmd) 
Error: processing vignette 'usaboundaries-sample-analysis.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'usaboundaries-sample-analysis.Rmd'

SUMMARY: processing the following file failed:
  'usaboundaries-sample-analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'readr'

Packages suggested but not available for checking:
  'tidyverse', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'usedist-Ex.R' failed
The error most likely occurred in:

> ### Name: pivot_to_numeric_matrix
> ### Title: Convert a data frame in long format to a numeric matrix
> ### Aliases: pivot_to_numeric_matrix
> 
> ### ** Examples
> 
> longdata <- data.frame(
+   SampleID = paste0("Sample", c(1, 1, 1, 2, 2, 3, 3)),
+   FeatureID = paste0("Feature", c(1, 2, 3, 1, 2, 2, 3)),
+   Value = c(132, 41, 7, 56, 11, 929, 83))
> longdata
  SampleID FeatureID Value
1  Sample1  Feature1   132
2  Sample1  Feature2    41
3  Sample1  Feature3     7
4  Sample2  Feature1    56
5  Sample2  Feature2    11
6  Sample3  Feature2   929
7  Sample3  Feature3    83
> pivot_to_numeric_matrix(longdata, SampleID, FeatureID, Value)
Error: Packages "dplyr", "tidyr", "tibble" are not installed, but are needed by "usedist::pivot_to_numeric_matrix".  Please install the missing packages to use this function.
Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

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:
  'tune', 'cli', 'recipes', '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: 'cli', 'gh'

Packages suggested but not available for checking:
  'roxygen2', 'styler', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'tsibble'

Packages suggested but not available for checking:
  'devtools', 'plotly', 'tidyr', 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'GGally', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'usmap-Ex.R' failed
The error most likely occurred in:

> ### Name: .east_north_central
> ### Title: East North Central census division
> ### Aliases: .east_north_central
> ### Keywords: datasets
> 
> ### ** Examples
> 
> plot_usmap(include = .east_north_central, labels = TRUE)
Error in plot_usmap(include = .east_north_central, labels = TRUE) : 
  `ggplot2` must be installed to use `plot_usmap`.
         Use: install.packages("ggplot2") and try again.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'advanced-mapping.Rmd' using rmarkdown
Quitting from lines 26-27 (advanced-mapping.Rmd) 
Error: processing vignette 'advanced-mapping.Rmd' failed with diagnostics:
`ggplot2` must be installed to use `plot_usmap`.
         Use: install.packages("ggplot2") and try again.
--- failed re-building 'advanced-mapping.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 26-27 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
`ggplot2` must be installed to use `plot_usmap`.
         Use: install.packages("ggplot2") and try again.
--- failed re-building 'introduction.Rmd'

--- re-building 'mapping.Rmd' using rmarkdown
Quitting from lines 24-31 (mapping.Rmd) 
Error: processing vignette 'mapping.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'mapping.Rmd'

SUMMARY: processing the following files failed:
  'advanced-mapping.Rmd' 'introduction.Rmd' 'mapping.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: 'broom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'ggdag'
Packages required but not available:
  'readr', 'biomaRt', 'vcfR', 'dplyr', 'tidyr', 'AnnotationHub',
  'ensembldb', 'GenomicFeatures', 'rtracklayer'

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:
  'haven', 'ggplot2', 'tibble', 'tidyr', 'dplyr', 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'engine.R'
  Comparing 'engine.Rout' to 'engine.Rout.save' ...4d3
< Using V8 engine 9.0.257.17
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'vaers', 'vaersND', 'dplyr'
Packages suggested but not available for checking:
  'vaers', 'vaersND', 'dplyr', 'pivottabler'
Packages required but not available:
  'GenomicAlignments', 'Rsamtools', 'ggplot2', 'ggplotify', 'ggpubr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tibble', 'tidyr', 'sf', 'leaflet', 'ggplot2', 'ggspatial',
  'geojsonio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'readr', 'tibble', 'broom', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'bench', 'tidyr', 'devtools', 'cowplot', 'dbplyr',
  'RMariaDB'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cowplot', 'ggplot2'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'EFA.MRFA', 'semPlot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'Seurat', 'sctransform'
Packages required but not available: 'dplyr', 'readr', 'sf', 'tibble'

Packages suggested but not available for checking:
  'ggplot2', 'lwgeom', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: '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', 'ggplot2', 'tidyverse', 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/vapour/vapour.Rcheck/00install.out' for details.
Packages required but not available: 'tibble', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Part of the varbvs package, https://github.com/pcarbo/varbvs
  > #
  > # Copyright (C) 2012-2018, Peter Carbonetto
  > #
  > # This program is free software: you can redistribute it under the
  > # terms of the GNU General Public License; either version 3 of the
  > # License, or (at your option) any later version.
  > #
  > # This program is distributed in the hope that it will be useful, but
  > # WITHOUT ANY WARRANY; without even the implied warranty of
  > # MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  > # General Public License for more details.
  > #
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'sparsevar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rstan', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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.
Package required but not available: 'sf'

Package suggested but not available for checking: 'RFmerge'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'varrank.Rmd' using knitr
Quitting from lines 79-91 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building 'varrank.Rmd'

SUMMARY: processing the following file failed:
  'varrank.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages unavailable to check Rd xrefs: 'car', 'candisc'
Running examples in 'VARSEDIG-Ex.R' failed
The error most likely occurred in:

> ### Name: VARSEDIG
> ### Title: Variable selection to discriminate among taxonomic groups
> ### Aliases: VARSEDIG
> ### Keywords: VARSEDIG
> 
> ### ** Examples
> 
> 
> data(characiformes)
> 
> VARSEDIG(data = characiformes , variables = c("M2","M3","M4","M5","M6","M7","M8","M9","M10",
+ "M11","M12","M13","M14","M15","M16","M17","M18","M19","M20","M21","M22","M23",
+ "M24","M25","M26","M27","M28"), group="Species" , group1= "Moenkhausia oligolepis",
+ group2="Moenkhausia dichroura", LEGENDd=c("x='topright'", "legend = dati",
+ "col = COLORB", "lty=lty", "bty='n'", "cex=1.2", "text.font= 3"),
+ LEGENDs=c("x='topright'", "legend=unique(datosF[,'Group'])", "col = color1",
+ "pch = pcht", "bty='n'", "cex=1.2", "text.font=3"), LEGENDr=c("x='topright'",
+ "legend = dati", "col=col", "pch= c(16,16)", "bty='n'", "cex=1.2", "text.font=3"),
+ XLIMs=c(-1.2,1.2), YLIMs=c(-1.3,1.3), BIVTEST12=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), BIVTEST21=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), colbiv="blue", ellipse=TRUE, convex=FALSE)
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
Error in loadNamespace(x) : there is no package called 'car'
Calls: VARSEDIG ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'rio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'article_html_varshrink.Rmd' using rmarkdown
Quitting from lines 149-160 (article_html_varshrink.Rmd) 
Error: processing vignette 'article_html_varshrink.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'article_html_varshrink.Rmd'

SUMMARY: processing the following file failed:
  'article_html_varshrink.Rmd'

Error: Vignette re-building failed.
Execution halted
Package required but not available: 'lmeresampler'

Package suggested but not available for checking: 'EnvStats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'mlr', 'mlrMBO', 'smoof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggplot2', 'car', 'AER'
Errors in running code in vignettes:
when running code in 'vcd-tutorial.Rnw'

> set.seed(1071)

> library(vcdExtra)
Loading required package: vcd
Loading required package: grid
Loading required package: gnm

> library(ggplot2)

  When sourcing 'vcd-tutorial.R':
Error: there is no package called 'ggplot2'
Execution halted

  'vcd-tutorial.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'vcd-tutorial.Rnw' using Sweave
Loading required package: vcd
Loading required package: grid
Loading required package: gnm

Error: processing vignette 'vcd-tutorial.Rnw' failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'vcd-tutorial.Rnw'

SUMMARY: processing the following file failed:
  'vcd-tutorial.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'tibble'

Packages suggested but not available for checking:
  'adegenet', 'ggplot2', 'poppr', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'cli'
Packages suggested but not available for checking:
  'dplyr', 'pillar', 'pkgdown', 'testthat', 'tibble', 'waldo'
Error(s) in re-building vignettes:
--- re-building 'pillar.Rmd' using rmarkdown
Quitting from lines 12-13 (pillar.Rmd) 
Error: processing vignette 'pillar.Rmd' failed with diagnostics:
there is no package called 'pillar'
--- failed re-building 'pillar.Rmd'

--- re-building 's3-vector.Rmd' using rmarkdown
Quitting from lines 146-153 (s3-vector.Rmd) 
Error: processing vignette 's3-vector.Rmd' failed with diagnostics:
there is no package called 'tibble'
--- failed re-building 's3-vector.Rmd'

--- re-building 'stability.Rmd' using rmarkdown
--- finished re-building 'stability.Rmd'

--- re-building 'type-size.Rmd' using rmarkdown
--- finished re-building 'type-size.Rmd'

SUMMARY: processing the following files failed:
  'pillar.Rmd' 's3-vector.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'vcvComp-worked-example.Rmd' using rmarkdown
Quitting from lines 46-54 (vcvComp-worked-example.Rmd) 
Error: processing vignette 'vcvComp-worked-example.Rmd' failed with diagnostics:
there is no package called 'geomorph'
--- failed re-building 'vcvComp-worked-example.Rmd'

SUMMARY: processing the following file failed:
  'vcvComp-worked-example.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'drc', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'ggthemes', 'ggtern'
Package required but not available: 'testthat'

Packages suggested but not available for checking: 'ggplot2', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'dplyr', '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: 'qgraph'

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: 'biwavelet', 'fields'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'bipartite'
Packages suggested but not available for checking:
  'testthat', 'usethis', 'readr', 'tibble', 'dplyr'
Packages required but not available: 'taxlist', 'plotKML'

Packages suggested but not available for checking: 'devtools', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'testthat', 'usethis'
Namespace in Imports field not imported from: 'rlang'
  All declared Imports should be used.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat);
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'ggplot2', 'ggpolypath'
Packages required but not available: 'ggplot2', 'lmerTest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'coRdon', '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:
  'cowplot', 'ggplot2', 'ggpubr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sf', 'dplyr', 'cli', 'dbplyr'

Packages suggested but not available for checking: 'testthat', 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lidR', 'viridis'

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', 'ggplot2', 'cowplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'car'

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: 'testthat', 'network'
Package unavailable to check Rd xrefs: 'network'
Running 'additonalExampleRuns.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'tidyr', 'dplyr', 'testthat'
Running examples in 'vinereg-Ex.R' failed
The error most likely occurred in:

> ### Name: plot_effects
> ### Title: Plot marginal effects of a D-vine regression model
> ### Aliases: plot_effects
> 
> ### ** Examples
> 
> # simulate data
> x <- matrix(rnorm(200), 100, 2)
> y <- x %*% c(1, -2)
> dat <- data.frame(y = y, x = x, z = as.factor(rbinom(100, 2, 0.5)))
> 
> # fit vine regression model
> fit <- vinereg(y ~ ., dat)
> plot_effects(fit)
Error in plot_effects(fit) : 
  The 'ggplot2' package must be installed to plot.
Execution halted
Running examples in 'vioplot-Ex.R' failed
The error most likely occurred in:

> ### Name: vioplot
> ### Title: Violin Plot
> ### Aliases: vioplot violinplot vioplot.matrix violin.matrix
> ###   violinplot.matrix vioplot.list vioplot.data.frame vioplot.formula
> ###   vioplot.default
> ### Keywords: graphics plot violin
> 
> ### ** Examples
> 
> 
> # box- vs violin-plot
> par(mfrow=c(2,1))
> mu<-2
> si<-0.6
> bimodal<-c(rnorm(1000,-mu,si),rnorm(1000,mu,si))
> uniform<-runif(2000,-4,4)
> normal<-rnorm(2000,0,3)
> vioplot(bimodal,uniform,normal)
> boxplot(bimodal,uniform,normal)
> 
> # add to an existing plot
> x <- rnorm(100)
> y <- rnorm(100)
> plot(x, y, xlim=c(-5,5), ylim=c(-5,5))
> vioplot(x, col="tomato", horizontal=TRUE, at=-4, add=TRUE,lty=2, rectCol="gray")
> vioplot(y, col="cyan", horizontal=FALSE, at=-4, add=TRUE,lty=2)
> 
> # formula input
> data("iris")
> vioplot(Sepal.Length~Species, data = iris, main = "Sepal Length",
+         col=c("lightgreen", "lightblue", "palevioletred"))
> legend("topleft", legend=c("setosa", "versicolor", "virginica"),
+        fill=c("lightgreen", "lightblue", "palevioletred"), cex = 0.5)
> 
> data("diamonds", package = "ggplot2")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'ggplot2'
Calls: data -> find.package
Execution halted
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggbeeswarm'
Error(s) in re-building vignettes:
--- re-building 'methodComparison.Rnw' using Sweave
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Error: processing vignette 'methodComparison.Rnw' failed with diagnostics:
 chunk 18 (label = showDiamond) 
Error in loadNamespace(x) : there is no package called 'ggplot2'

--- failed re-building 'methodComparison.Rnw'

--- re-building 'usageExamples.Rnw' using Sweave

Error: processing vignette 'usageExamples.Rnw' failed with diagnostics:
 chunk 18 (label = showGg) 
Error in library(ggbeeswarm) : there is no package called 'ggbeeswarm'

--- failed re-building 'usageExamples.Rnw'

SUMMARY: processing the following files failed:
  'methodComparison.Rnw' 'usageExamples.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'tibble'

Packages suggested but not available for checking:
  'caret', 'dplyr', 'fastshap', 'mlr', 'NeuralNetTools', 'parsnip',
  'pdp', 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'viridisLite-Ex.R' failed
The error most likely occurred in:

> ### Name: viridis
> ### Title: Viridis Color Palettes
> ### Aliases: viridis viridisMap magma inferno plasma cividis rocket mako
> ###   turbo
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'vdiffr', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'viridis', 'tidyr'

Packages suggested but not available for checking: 'devtools', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'nycflights13', 'testthat', 'dplyr'
Packages suggested but not available for checking:
  'dplyr', 'tibble', 'tidyverse'
Running examples in 'visachartR-Ex.R' failed
The error most likely occurred in:

> ### Name: alluvial_diagram
> ### Title: alluvial_diagram
> ### Aliases: alluvial_diagram
> 
> ### ** Examples
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called 'tidyverse'
Execution halted
Packages required but not available: 'ggplot2', 'ggpmisc'

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:
  'ggplot2', 'tidyr', 'dplyr', 'readr', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'plotly', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'colourpicker', 'ggraph', 'tidygraph'
Packages required but not available:
  'broom', 'ggplot2', 'tidyr', 'dplyr', 'kableExtra', 'gt', 'parcats',
  'cowplot'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'forcats', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotly', 'ggplot2', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'highcharter'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'plotly'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'FactoMineR', 'ggplot2', 'dplyr', 'ggrepel'

Package suggested but not available for checking: 'egg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyr', 'ggplot2', 'ggdendro', 'ggrepel', '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', 'tibble', 'pillar'

Packages suggested but not available for checking: 'rorcid', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'condvis2', 'ggplot2', 'GGally', 'ggalt', 'dplyr', 'flashlight',
  'ggnewscale', 'tidyr'

Packages suggested but not available for checking:
  'intergraph', 'network', 'sna', 'mlr', 'tidymodels', 'lemon', 'vip',
  'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggplot2', 'DALEX'

Packages suggested but not available for checking:
  'testthat', 'ingredients'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggrepel', 'ggplot2', 'ggiraph', 'ggsci'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'ggmap', 'marmap', 'ggplot2', 'fields'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'plotly', 'ggplot2', 'ggpubr', 'ggrepel'

Packages suggested but not available for checking: 'kableExtra', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'ggplot2', 'tibble'
Error(s) in re-building vignettes:
--- re-building 'Datasets-for-Seminars.Rmd' using rmarkdown
Quitting from lines 20-35 (Datasets-for-Seminars.Rmd) 
Error: processing vignette 'Datasets-for-Seminars.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'Datasets-for-Seminars.Rmd'

--- re-building 'Introduction-to-volleystat.Rmd' using rmarkdown
Quitting from lines 20-30 (Introduction-to-volleystat.Rmd) 
Error: processing vignette 'Introduction-to-volleystat.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'Introduction-to-volleystat.Rmd'

SUMMARY: processing the following files failed:
  'Datasets-for-Seminars.Rmd' 'Introduction-to-volleystat.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggplot2', 'GGally'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'syuzhet', 'vosonSML'

Packages suggested but not available for checking: 'dplyr', 'rtweet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'Hmisc', 'rtweet', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'tidytext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'lmerTest', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'readr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'oce', 'dplyr', 'tidyr', 'metR', '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: 'cli', 'tibble'

Packages suggested but not available for checking:
  'archive', 'bench', 'dplyr', 'forcats', 'ggplot2', 'patchwork',
  'testthat', 'tidyr', 'waldo'

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', 'dplyr', 'survminer', 'flexsurv', 'ggpubr'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'xml2'
  All declared Imports should be used.
Packages required but not available: 'kableExtra', 'haven'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'plotKML', '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: 'DiagrammeR'

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: 'rvest', '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: 'packer'
Packages required but not available: 'cli', 'rematch2', '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:
  'bayesplot', 'rstan', 'dplyr', 'Hmisc', 'ggplot2', 'rstantools',
  'StanHeaders'

Packages suggested but not available for checking: 'diagis', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'leaflet', 'dplyr', 'ENMeval', 'leaflet.extras', 'spocc', 'spThin'

Packages suggested but not available for checking: 'rgbif', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'riskRegression'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'helper-functions.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: 'readtext'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'leaflet', 'kableExtra'
Package required but not available: 'dataRetrieval'

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:
  'testthat', 'tibble', 'tmap', 'tmaptools', 'OpenStreetMap', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'ggvoronoi', 'sf'
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 32-43 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'dplyr', 'spectacles', 'caret', 'ggplot2', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'examples.Rmd' using rmarkdown
Quitting from lines 36-51 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'examples.Rmd'

SUMMARY: processing the following file failed:
  'examples.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'cellWise'
Error(s) in re-building vignettes:
--- re-building 'wbacon.Rmd' using rmarkdown
Quitting from lines 173-175 (wbacon.Rmd) 
Error: processing vignette 'wbacon.Rmd' failed with diagnostics:
there is no package called 'cellWise'
--- failed re-building 'wbacon.Rmd'

SUMMARY: processing the following file failed:
  'wbacon.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'readr', 'tibble', 'tidyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tibble', 'readr', 'forcats', 'tidyverse', 'lemon'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'arcpullr', 'sf', '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: 'sf', 'cli', 'lwgeom', 'tibble'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'ggmap', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'RHRV', 'padr', 'varian', '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: 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rvest', 'dplyr', 'tibble'

Packages suggested but not available for checking: 'testthat', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'geojsonio'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

Packages suggested but not available for checking:
  'iptools', 'rgeolocate', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'moonBook', 'ggplot2', 'rrtable', 'dplyr', 'tibble', 'tidyr',
  'ggforce'

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', 'sf'

Packages suggested but not available for checking: 'testthat', 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'haven'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'readxl', 'dplyr', 'tidytext', 'tibble', 'tidyr', 'forcats',
  'ggplot2', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'tibble', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'WeightedROC-Ex.R' failed
The error most likely occurred in:

> ### Name: WeightedROC
> ### Title: WeightedROC
> ### Aliases: WeightedROC
> 
> ### ** Examples
> 
> 
> ## WeightedROC can compute ROC curves for data sets with variable
> ## weights.
> library(WeightedROC)
> y <- c(-1, -1, 1, 1, 1)
> w <- c(1, 1, 1, 4, 5)
> y.hat <- c(1, 2, 3, 1, 1)
> tp.fp <- WeightedROC(y.hat, y, w)
> if(require(ggplot2)){
+   gg <- ggplot()+
+     geom_path(aes(FPR, TPR), data=tp.fp)+
+     coord_equal()
+   print(gg)
+ }else{
+   plot(TPR~FPR, tp.fp, type="l")
+ }
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
> 
> ## The FN/FP columns can be used to plot weighted error as a
> ## function of threshold.
> error.fun.list <- list(
+   FN=function(df)df$FN,
+   FP=function(df)df$FP,
+   errors=function(df)with(df, FP+FN)
+   )
> all.error.list <- list()
> for(error.type in names(error.fun.list)){
+   error.fun <- error.fun.list[[error.type]]
+   all.error.list[[error.type]] <-
+     data.frame(tp.fp, error.type, weighted.error=error.fun(tp.fp))
+ }
> all.error <- do.call(rbind, all.error.list)
> fp.fn.colors <- c(FP="skyblue",
+                   FN="#E41A1C",
+                   errors="black")
> ggplot()+
+   scale_color_manual(values=fp.fn.colors)+
+   geom_line(aes(threshold, weighted.error, color=error.type),
+             data=all.error)
Error in ggplot() : could not find function "ggplot"
Execution halted
Errors in running code in vignettes:
when running code in 'Definition.Rnw'

> y <- c(-1, -1, 1, 1, 1)

> w <- c(1, 1, 1, 4, 5)

> y.hat <- c(1, 2, 3, 1, 1)

> library(WeightedROC)

> tp.fp <- WeightedROC(y.hat, y, w)

> library(ggplot2)

  When sourcing 'Definition.R':
Error: there is no package called 'ggplot2'
Execution halted

  'Definition.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'Definition.Rnw' using Sweave

Error: processing vignette 'Definition.Rnw' failed with diagnostics:
 chunk 1 (label = curve) 
Error in library(ggplot2) : there is no package called 'ggplot2'

--- failed re-building 'Definition.Rnw'

SUMMARY: processing the following file failed:
  'Definition.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'cobalt', 'ggplot2'

Packages suggested but not available for checking:
  'twang', 'optweight', 'mlogit', 'mclogit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'mice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'wellknown-Ex.R' failed
The error most likely occurred in:

> ### Name: multilinestring
> ### Title: Make WKT multilinestring objects
> ### Aliases: multilinestring
> 
> ### ** Examples
> 
> ## empty multilinestring
> multilinestring("empty")
[1] "MULTILINESTRING EMPTY"
> # multilinestring("stuff")
> 
> # character string
> x <- "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> multilinestring(x)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> 
> # data.frame
> df <- data.frame(long = c(30, 45, 10), lat = c(20, 40, 40))
> df2 <- data.frame(long = c(15, 40, 10), lat = c(5, 10, 20))
> multilinestring(df, df2, fmt=0)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> lint(multilinestring(df, df2, fmt=0))
[1] TRUE
> wktview(multilinestring(df, df2), zoom=3)
Error: Please install leaflet
Execution halted
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library('testthat')
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: 'NPflow'

Packages suggested but not available for checking: 'testthat', 'EdSurvey'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'geepack', 'CRTgeeDR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'cli'

Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', '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:
  'plotly', 'shinyFiles', 'readr', 'readxl', 'testthat', 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'tidyr', 'tidytext', 'broom'

Packages suggested but not available for checking:
  'ggraph', 'gapminder', 'testthat', 'fuzzyjoin', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'readr'

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', 'readr'

Packages suggested but not available for checking: 'testthat', 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'WikidataQueryServiceR', 'tibble', 'dplyr', 'Hmisc', 'readr'

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: 'rvest', '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: 'rvest', 'ggplot2'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(WikipediR)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'WikidataR', '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', 'sf'

Packages suggested but not available for checking:
  'ggplot2', 'GGally', 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'colourpicker', 'viridis', 'ggrepel', 'DESeq2',
  'FactoMineR', 'factoextra', 'heatmaply'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  trace_back_backtrace.c:87:19: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/winch/winch.Rcheck/00install.out' for details.
Running 'example0.R'
  Running 'example1.R'
  Running 'example2.R'
  Running 'example3.R'
  Running 'example4.R'
  Running 'example5.R'
  Running 'example6.R'
  Running 'example7.R'
  Running 'example8.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'drc', 'imputeTestbench'

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 'basics.Rmd' using rmarkdown
Quitting from lines 52-65 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'basics.Rmd'

SUMMARY: processing the following file failed:
  'basics.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'testthat', 'rnrfa'
Packages required but not available: 'tidyverse', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'secr'
Package unavailable to check Rd xrefs: 'secr'
Packages required but not available: 'HydeNet', 'dplyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'testthat', 'sf', 'tibble'
Packages required but not available: 'tibble', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'LindleyR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'Introductory-Econometrics-Examples.Rmd' using rmarkdown

Please cite as: 

 Hlavac, Marek (2018). stargazer: Well-Formatted Regression and Summary Statistics Tables.
 R package version 5.2.2. https://CRAN.R-project.org/package=stargazer 

Quitting from lines 943-945 (Introductory-Econometrics-Examples.Rmd) 
Error: processing vignette 'Introductory-Econometrics-Examples.Rmd' failed with diagnostics:
there is no package called 'AER'
--- failed re-building 'Introductory-Econometrics-Examples.Rmd'

SUMMARY: processing the following file failed:
  'Introductory-Econometrics-Examples.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dbplyr', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidygraph', 'tibble', 'ggraph', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Packages required but not available: 'ggplot2', 'patchwork', 'dplyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'spelling.R'
  Running 'system-info.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'cli', 'dplyr', 'ggplot2', 'hardhat', 'rsample', 'tibble', 'tidyr',
  'tune', 'workflows'

Packages suggested but not available for checking:
  'dials', 'parsnip', 'recipes', 'testthat', 'yardstick'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'cli', 'hardhat', 'parsnip'

Packages suggested but not available for checking:
  'butcher', 'recipes', 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'Analyzing-workloops.Rmd' using rmarkdown
Quitting from lines 27-31 (Analyzing-workloops.Rmd) 
Error: processing vignette 'Analyzing-workloops.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Analyzing-workloops.Rmd'

--- re-building 'Calculating-twitch-kinetics.Rmd' using rmarkdown
Quitting from lines 28-31 (Calculating-twitch-kinetics.Rmd) 
Error: processing vignette 'Calculating-twitch-kinetics.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Calculating-twitch-kinetics.Rmd'

--- re-building 'Introduction-to-workloopR.Rmd' using rmarkdown
--- finished re-building 'Introduction-to-workloopR.Rmd'

--- re-building 'Plotting-workloopR.Rmd' using rmarkdown
Quitting from lines 25-31 (Plotting-workloopR.Rmd) 
Error: processing vignette 'Plotting-workloopR.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'Plotting-workloopR.Rmd'

--- re-building 'batch-processing.Rmd' using rmarkdown

Attaching package: 'purrr'

The following object is masked from 'package:magrittr':

    set_names

Quitting from lines 137-139 (batch-processing.Rmd) 
Error: processing vignette 'batch-processing.Rmd' failed with diagnostics:
`map_df()` requires dplyr
--- failed re-building 'batch-processing.Rmd'

--- re-building 'non-ddf-sources.Rmd' using rmarkdown
Quitting from lines 29-32 (non-ddf-sources.Rmd) 
Error: processing vignette 'non-ddf-sources.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'non-ddf-sources.Rmd'

SUMMARY: processing the following files failed:
  'Analyzing-workloops.Rmd' 'Calculating-twitch-kinetics.Rmd'
  'Plotting-workloopR.Rmd' 'batch-processing.Rmd' 'non-ddf-sources.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'openair', 'dplyr', 'leaflet', 'tidyr', 'readr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: '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', 'ggrepel', 'tidytext', 'ggraph',
  'ggwordcloud'

Package suggested but not available for checking: 'portes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'tidyverse', 'dplyr', 'forcats', 'ggplot2', 'tibble', 'tidyr',
  'kableExtra'

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', 'factoextra', 'FactoMineR'
Error(s) in re-building vignettes:
--- re-building 'wrGraphVignette1.Rmd' using rmarkdown
Quitting from lines 27-33 (wrGraphVignette1.Rmd) 
Error: processing vignette 'wrGraphVignette1.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building 'wrGraphVignette1.Rmd'

SUMMARY: processing the following file failed:
  'wrGraphVignette1.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'fdapace', 'fdadensity', '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:
  'readxl', 'nycflights13', 'testthat'
Running examples in 'writexl-Ex.R' failed
The error most likely occurred in:

> ### Name: write_xlsx
> ### Title: Export to xlsx
> ### Aliases: write_xlsx writexl
> 
> ### ** Examples
> 
> # Roundtrip example with single excel sheet named 'mysheet'
> tmp <- write_xlsx(list(mysheet = iris))
> readxl::read_xlsx(tmp)
Error in loadNamespace(x) : there is no package called 'readxl'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages suggested but not available for checking:
  'qvalue', 'readxl', 'vsn'
Packages unavailable to check Rd xrefs: 'vsn', 'readxl'
Running examples in 'wrMisc-Ex.R' failed
The error most likely occurred in:

> ### Name: readXlsxBatch
> ### Title: Read batch of Excel xlsx-files
> ### Aliases: readXlsxBatch
> 
> ### ** Examples
> 
> path1 <- system.file("extdata", package="wrMisc")
> fiNa <- c("pl01_1.xlsx","pl01_2.xlsx","pl02_1.xlsx","pl02_2.xlsx")
> datAll <- readXlsxBatch(fiNa, path1)
Error in readXlsxBatch(fiNa, path1) : 
   -> readXlsxBatch : package 'readxl' not found ! Please install first
Execution halted
Error(s) in re-building vignettes:
--- re-building 'wrProteoVignette1.Rmd' using rmarkdown
--- finished re-building 'wrProteoVignette1.Rmd'

--- re-building 'wrProteoVignetteUPS1.Rmd' using rmarkdown
Quitting from lines 246-251 (wrProteoVignetteUPS1.Rmd) 
Error: processing vignette 'wrProteoVignetteUPS1.Rmd' failed with diagnostics:
 -> readProlineFile : package 'readxl' not found ! Please install first
--- failed re-building 'wrProteoVignetteUPS1.Rmd'

SUMMARY: processing the following file failed:
  'wrProteoVignetteUPS1.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'car', 'ggplot2', 'mediation', 'GGally'
Error(s) in re-building vignettes:
--- re-building 'WRS2.Rnw' using knitr
kpsewhich: major issue: User/administrator updates are out-of-sync.
Quitting from lines 194-195 (WRS2.Rnw) 
Error: processing vignette 'WRS2.Rnw' failed with diagnostics:
there is no package called 'GGally'
--- failed re-building 'WRS2.Rnw'

SUMMARY: processing the following file failed:
  'WRS2.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Hmisc', 'ggplot2', 'GGally', 'network'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'caret', 'dplyr', 'fields', 'forecast', 'tidyr'

Packages suggested but not available for checking: 'EGRET', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'fields'

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: 'fields', 'Hmisc', 'rworldmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Package suggested but not available for checking: 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sde', 'ftsa', 'rainbow'

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', 'wyz.code.offensiveProgramming'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/x13binary/x13binary.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'ggplot2-themes.Rmd' using rmarkdown
Quitting from lines 101-110 (ggplot2-themes.Rmd) 
Error: processing vignette 'ggplot2-themes.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'ggplot2-themes.Rmd'

--- re-building 'template-variables.Rmd' using rmarkdown
--- finished re-building 'template-variables.Rmd'

--- re-building 'xaringanthemer.Rmd' using rmarkdown
Quitting from lines 59-70 (./../man/fragments/_quick-intro.Rmd) 
Quitting from lines 59-70 (./../man/fragments/_quick-intro.Rmd) 
Error: processing vignette 'xaringanthemer.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'xaringanthemer.Rmd'

SUMMARY: processing the following files failed:
  'ggplot2-themes.Rmd' 'xaringanthemer.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'bupaR', 'dplyr', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pak'
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testit)
  > test_pkg('xfun')
  
  Attaching package: 'xfun'
  
  The following objects are masked from 'package:base':
  
      attr, isFALSE
  
  assertion failed: native_encode() warns against characters that cannot be represented in native encoding
  Error from assert("native_encode() warns against characters that cannot be represented in native encoding",  ...  at test-encoding.R#3 
  Error: (!is_windows() || has_warning({ ....  is not TRUE
  Execution halted
Running examples in 'xgb2sql-Ex.R' failed
The error most likely occurred in:

> ### Name: booster2sql
> ### Title: Transform XGBoost model object to SQL query.
> ### Aliases: booster2sql
> 
> ### ** Examples
> 
> library(xgboost)
> # load data
> df = data.frame(ggplot2::diamonds)
Error in loadNamespace(x) : there is no package called 'ggplot2'
Calls: data.frame ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'xgb2sql.Rmd' using rmarkdown
Quitting from lines 62-67 (xgb2sql.Rmd) 
Error: processing vignette 'xgb2sql.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'xgb2sql.Rmd'

SUMMARY: processing the following file failed:
  'xgb2sql.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ggplot2', 'DiagrammeR', 'testthat', 'lintr'
Packages required but not available:
  'dplyr', 'ggplot2', 'Hmisc', 'readr', 'tibble'

Packages suggested but not available for checking:
  'pkgdown', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'psychTools'
  All declared Imports should be used.
Running examples in 'XICOR-Ex.R' failed
The error most likely occurred in:

> ### Name: xicor
> ### Title: Compute the cross rank increment correlation coefficient xi.
> ### Aliases: xicor xi
> ### Keywords: ~htest ~methods
> 
> ### ** Examples
> 
> 
> ##---- Should be DIRECTLY executable !! ----
> library("psychTools")
> data(peas)
> # Visualize       the peas data
> library(ggplot2)
Error in library(ggplot2) : there is no package called 'ggplot2'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ./testthat
  > 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_check("XiMpLe")
  Error in test_check("XiMpLe") : could not find function "test_check"
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'XLConnect.Rnw' using Sweave
Loading required package: XLConnect
XLConnect 1.0.4 by Mirai Solutions GmbH [aut],
  Martin Studer [cre],
  The Apache Software Foundation [ctb, cph] (Apache POI),
  Graph Builder [ctb, cph] (Curvesapi Java library),
  Brett Woolridge [ctb, cph] (SparseBitSet Java library)
https://mirai-solutions.ch
https://github.com/miraisolutions/xlconnect
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'

Error: processing vignette 'XLConnect.Rnw' failed with diagnostics:
 chunk 20 (label = AdvancedExampleP5) 
Error in ggplot(gcurr, aes(Date, Value, colour = Currency)) : 
  could not find function "ggplot"

--- failed re-building 'XLConnect.Rnw'

--- re-building 'XLConnectImpatient.Rnw' using Sweave
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
--- finished re-building 'XLConnectImpatient.Rnw'

Warning in file.remove(f) :
  cannot remove file 'XLConnectExample1.xlsx', reason 'Permission denied'
Warning in file.remove(f) :
  cannot remove file 'XLConnectExample3.xlsx', reason 'Permission denied'
Warning in file.remove(f) :
  cannot remove file 'swiss_franc.xlsx', reason 'Permission denied'
SUMMARY: processing the following file failed:
  'XLConnect.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'tidyr', '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:
  'testthat', 'ChemmineR', 'fmcsR'
Package required but not available: 'readr'

Package suggested but not available for checking: 'car'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'blorr', 'descriptr', 'haven', 'highcharter', 'kableExtra', 'olsrr',
  'plotly', 'rbokeh', 'readr', 'readxl', 'rfm', 'vistributions'
Packages required but not available:
  'FactoMineR', 'ggplot2', 'ggdendro', 'ggforce', 'ggrepel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'Hmisc', 'dplyr', 'tibble', 'readr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'xpose', 'ggplot2', 'nlmixr', 'dplyr', 'tibble', 'tidyr', 'vpc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'ggforce', 'readr', 'tibble', 'tidyr', 'vpc'

Packages suggested but not available for checking: 'testthat', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'dplyr', 'fuzzyjoin'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'colourpicker'

Packages suggested but not available for checking:
  'testthat', 'shinyFiles', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'pdp', 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking:
  'factorMerger', 'testthat', 'caret', 'breakDown', 'DALEX'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'bench'
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
Quitting from lines 73-78 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'bench'
--- 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: 'spork', 'ggplot2', 'dplyr', 'tidyr'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # browseURL("https://kbroman.org/pkg_primer/pages/tests.html")
  > # browseURL(file.path("https://walczak.org/2017/06",
  > # 		"how-to-add-code-coverage-codecov-to-your-r-package/"))
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'cowplot', 'ggplot2', 'ggrepel', 'viridis'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'probably', 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggtree', 'testthat'
Error(s) in re-building vignettes:
--- re-building 'gammaproteobacteria.Rmd' using rmarkdown
Quitting from lines 24-27 (gammaproteobacteria.Rmd) 
Error: processing vignette 'gammaproteobacteria.Rmd' failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building 'gammaproteobacteria.Rmd'

SUMMARY: processing the following file failed:
  'gammaproteobacteria.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'MBESS'
Package required but not available: 'usethis'

Packages suggested but not available for checking:
  'pkgdown', '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: 'testthat', 'tidyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'sde', 'ggplot2', 'plotly'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > require(testthat);
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > require(here);
  Loading required package: here
  here() starts at C:/msys64/home/tomas/ucrt3/svn/ucrt3
  > test_check("yum");
  Error in test_check("yum") : could not find function "test_check"
  Execution halted
Package required but not available: 'dplyr'

Packages suggested but not available for checking:
  'RNRCS', 'metScanR', 'rnoaa', 'neonUtilities'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggplot2'

Packages suggested but not available for checking: 'devtools', 'usethis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'lomb'

Packages suggested but not available for checking:
  'testthat', 'ggetho', 'damr', 'xsp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'AER', 'dplyr', 'geepack'

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', 'questionr', 'ggplot2', 'plotly', 'viridis', 'hrbrthemes'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'tidycensus', 'tidyr', 'dplyr'

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', 'testthat', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'ggthemes', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using knitr
Quitting from lines 44-51 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'zlog.Rmd' using rmarkdown
Quitting from lines 65-105 (zlog.Rmd) 
Error: processing vignette 'zlog.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'zlog.Rmd'

SUMMARY: processing the following file failed:
  'zlog.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'readr', 'mockery', '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', 'zdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'sf'

Packages suggested but not available for checking:
  'tmap', 'tmaptools', 'pct', 'dplyr', 'lwgeom', 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
--- re-building 'index.Rmd' using rmarkdown
Quitting from lines 345-346 (index.Rmd) 
Error: processing vignette 'index.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building 'index.Rmd'

SUMMARY: processing the following file failed:
  'index.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dplyr', 'syuzhet'

Package suggested but not available for checking: 'testthat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testall.R'
Running the tests in 'tests/testall.R' failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'rfigshare', 'roxygen2', 'rworldmap', 'testthat'

Package suggested but not available for checking: 'SDMTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'AER', 'ggplot2'
Packages suggested but not available for checking: 'moonBook', 'testthat'
Running examples in 'ztable-Ex.R' failed
The error most likely occurred in:

> ### Name: totalLeft
> ### Title: Arrange total column to the left
> ### Aliases: totalLeft
> 
> ### ** Examples
> 
> require(moonBook)
Loading required package: moonBook
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moonBook'
> require(ztable)
> require(magrittr)
Loading required package: magrittr
> mytable(sex~.,data=acs,show.total=TRUE) %>% ztable() %>% totalLeft()
Error in mytable(sex ~ ., data = acs, show.total = TRUE) : 
  could not find function "mytable"
Calls: %>% -> totalLeft -> %in% -> ztable
Execution halted
Error(s) in re-building vignettes:
--- re-building 'heatmapTable.Rmd' using rmarkdown
Loading required package: moonBook
Quitting from lines 40-43 (heatmapTable.Rmd) 
Error: processing vignette 'heatmapTable.Rmd' failed with diagnostics:
object 'acs' not found
--- failed re-building 'heatmapTable.Rmd'

--- re-building 'ztable.Rmd' using rmarkdown
Warning in data(colon) : data set 'colon' not found
Quitting from lines 435-442 (ztable.Rmd) 
Error: processing vignette 'ztable.Rmd' failed with diagnostics:
could not find function "mytable"
--- failed re-building 'ztable.Rmd'

--- re-building 'ztable_update.Rmd' using rmarkdown
--- finished re-building 'ztable_update.Rmd'

SUMMARY: processing the following files failed:
  'heatmapTable.Rmd' 'ztable.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'testthat', 'tidyr'
Error(s) in re-building vignettes:
--- re-building 'ztpln.rmd' using rmarkdown
Quitting from lines 102-110 (ztpln.rmd) 
Error: processing vignette 'ztpln.rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building 'ztpln.rmd'

SUMMARY: processing the following file failed:
  'ztpln.rmd'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rvest', 'dplyr', 'ggplot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'dplyr'

Packages suggested but not available for checking: 'ggplot2', 'ggthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'httptest', 'roxygen2', 'testthat'
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cairoDevice.Rcheck/00install.out’ for details.
---- unloading

 *** caught segfault ***
address 0x7f901d5d5c30, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Running ‘testthat.R’ [3s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GBcurves)
  > 
  > test_check("GBcurves")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_gb.R:23:3): Test function ─────────────────────────────────────
  nrow(df.out) > 0 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘.gitlab-ci.yml’
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Dependence on R version ‘3.6.2’ not with patchlevel 0
Running ‘exporting-methods.R’ [3s/4s]
  Running ‘testthat.R’ [34s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.match_on.R:591:5): standardization_scale with svyglm ────────────
  Error: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   └─optmatch:::standardizer(des_t)
   3.     ├─stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     └─survey:::update.survey.design(...)
   5.       └─base::eval(dots[[j]], object$variables, parent.frame())
   6.         └─base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("pestr")
  > 
  > test_check("pestr")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_dbnameextraction.R:24:3): Test that f returns correct names from database ──
  Error: use of NULL environment is defunct
  Backtrace:
       █
    1. ├─testthat::expect_equal(...) test_dbnameextraction.R:24:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─pestr::eppo_names_tables(testNames)
    5. │ ├─base::data.frame(...)
    6. │ └─`%>%`(...)
    7. ├─dplyr::left_join(., EPPOcodes, by = "codeid")
    8. ├─dplyr::select(., -.data$status)
    9. ├─dplyr:::select.data.frame(., -.data$status)
   10. │ └─tidyselect::eval_select(expr(c(...)), .data)
   11. │   └─tidyselect:::eval_select_impl(...)
   12. │     ├─tidyselect:::with_subscript_errors(...)
   13. │     │ ├─base::tryCatch(...)
   14. │     │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
   15. │     │ │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   16. │     │ │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
   17. │     │ └─tidyselect:::instrument_base_errors(expr)
   18. │     │   └─base::withCallingHandlers(...)
   19. │     └─tidyselect:::vars_select_eval(...)
   20. │       └─rlang::new_data_mask(env(!!!vars_select_helpers))
   21. ├─(function (hash = TRUE, parent = parent.frame(), size = 29L) ...
   22. └─base::.handleSimpleError(...)
   23.   └─tidyselect:::h(simpleError(msg, call))
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 78 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(piggyback)
  > Sys.setenv(piggyback_cache_duration=0)
  > test_check("piggyback")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (16)
  • piggyback:::get_token() == "b2b7441daeeb010b1df26f1f60a7f1edc485e443" is TRUE (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-on-cran.R:7:5): we can list files even from CRAN ────────────────
  Error: Cannot access release data for repository cboettig/piggyback-tests. Check that you have set a GITHUB_TOKEN and that at least one release on your GitHub repository page.
  Backtrace:
       █
    1. └─piggyback::pb_list(repo = "cboettig/piggyback-tests", tag = "v0.0.1") test-on-cran.R:7:4
    2.   └─piggyback:::pb_info(repo, tag, .token)
    3.     ├─piggyback:::memoised_pb_info(repo, tag, .token)
    4.     │ ├─base::withVisible(eval(mc, parent.frame()))
    5.     │ └─base::eval(mc, parent.frame())
    6.     │   └─base::eval(mc, parent.frame())
    7.     └─(function (repo = guess_repo(), tag = NULL, .token = get_token()) ...
    8.       └─piggyback:::release_info(repo, .token)
    9.         └─piggyback:::maybe(...)
   10.           └─base::tryCatch(...)
   11.             └─base:::tryCatchList(expr, classes, parentenv, handlers)
   12.               └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13.                 └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 8 | SKIP 21 | PASS 3 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘alternatives.Rmd’ using rmarkdown
--- finished re-building ‘alternatives.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 130-132 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Cannot access release data for repository cboettig/piggyback-tests. Check that you have set a GITHUB_TOKEN and that at least one release on your GitHub repository page.
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RDieHarder.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
  standalone.c:220:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Dependence on R version ‘3.6.3’ not with patchlevel 0
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
--- finished re-building ‘intro.Rmd’

--- re-building ‘united_nations.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 81-92 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
Can't join on `x$a2` x `y$a2` because of incompatible types.
ℹ `x$a2` is of type <logical>>.
ℹ `y$a2` is of type <character>>.
--- failed re-building ‘united_nations.Rmd’

SUMMARY: processing the following file failed:
  ‘united_nations.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘aaSEA_Documentation.Rmd’

SUMMARY: processing the following file failed:
  ‘aaSEA_Documentation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets  12.2Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  14.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.6Mb
    data       2.8Mb
    pictures   2.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    data    1.3Mb
    files   1.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Packages suggested but not available for checking: 'rsvg', 'AdhereRViz'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘qpAdm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
ADMIXTOOLS programs required by admixr are not in your $PATH variable.
At the very least, the following programs should be available:
    qp3Pop, qpDstat, qpF4ratio, qpAdm, qpWave
Make sure to modify the $PATH variable in your .Renviron file so 
that it points to the directory containing the ADMIXTOOLS programs.

Quitting from lines 131-134 (qpAdm.Rmd) 
Error: processing vignette 'qpAdm.Rmd' failed with diagnostics:
'wget' call had nonzero exit status
--- failed re-building ‘qpAdm.Rmd’

--- re-building ‘tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
ADMIXTOOLS programs required by admixr are not in your $PATH variable.
At the very least, the following programs should be available:
    qp3Pop, qpDstat, qpF4ratio, qpAdm, qpWave
Make sure to modify the $PATH variable in your .Renviron file so 
that it points to the directory containing the ADMIXTOOLS programs.

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 132-133 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'wget' call had nonzero exit status
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘qpAdm.Rmd’ ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    tutorials   6.1Mb
Package suggested but not available for checking: ‘glmmTMB’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ahn.Rmd’

SUMMARY: processing the following file failed:
  ‘ahn.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ggseas’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.6Mb
Package suggested but not available for checking: ‘rsvg’
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.5Mb
Package suggested but not available for checking: ‘ssh’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    test_v8    2.1Mb
    testdata   2.4Mb
Package suggested but not available for checking: ‘kebabs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘apcluster.Rnw’ using knitr

Attaching package: 'apcluster'

The following object is masked from 'package:stats':

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
--- failed re-building ‘apcluster.Rnw’

SUMMARY: processing the following file failed:
  ‘apcluster.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
Package suggested but not available for checking: ‘qCBA’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
Package suggested but not available for checking: ‘RWeka’
Package suggested but not available for checking: ‘REBayes’
Error(s) in re-building vignettes:
  ...
--- re-building ‘asmapvignette.Rnw’ using knitr
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    full_doc   2.6Mb
Package required but not available: ‘seasonal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aweSOM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-101 (aweSOM.Rmd) 
Error: processing vignette 'aweSOM.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘aweSOM.Rmd’

SUMMARY: processing the following file failed:
  ‘aweSOM.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘RestRserve’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.4Mb
Running examples in ‘bagged.outliertrees-Ex.R’ failed
The error most likely occurred in:

> ### Name: bagged.outliertrees
> ### Title: Bagged OutlierTrees
> ### Aliases: bagged.outliertrees
> 
> ### ** Examples
> 
> library(bagged.outliertrees)
> 
> ### example dataset with interesting outliers
> data(hypothyroid)
> 
> ### fit a Bagged OutlierTrees model
> model <- bagged.outliertrees(hypothyroid,
+   ntrees = 10,
+   subsampling_rate = 0.5,
+   z_outlier = 6,
+   nthreads = 1
+ )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%Error in unserialize(socklist[[n]]) : error reading from connection
Calls: bagged.outliertrees ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Found the following files/directories:
  ‘core’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.2Mb
    doc    1.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘article4.Rnw’ using knitr
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   5.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
    libs   1.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BLE_Categorical.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BLE_Categorical.Rmd’

--- re-building ‘BLE_Ratio.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BLE_Ratio.Rmd’

--- re-building ‘BLE_Reg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BLE_Reg.Rmd’

--- re-building ‘BLE_SRS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BLE_SRS.Rmd’

--- re-building ‘BLE_SSRS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 87-95 (BLE_SSRS.Rmd) 
Error: processing vignette 'BLE_SSRS.Rmd' failed with diagnostics:
cannot allocate vector of size 753.8 Mb
--- failed re-building ‘BLE_SSRS.Rmd’

--- re-building ‘BayesSampling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BayesSampling.Rmd’

SUMMARY: processing the following file failed:
  ‘BLE_SSRS.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    help   1.3Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Running ‘testthat.R’ [24s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.11.1 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  ===== Monitors =====
  thin = 1: tau, betalpha
  ===== Samplers =====
  conjugate sampler (5)
    - tau
    - betalpha[]  (4 elements)
  RW sampler (10)
    - betalpha[]  (10 elements)
  thin = 1: tau, betalpha, sigma, eta
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (testthat.R:3:1): (code run outside of `test_that()`) ─────────────────
  Error: Failed to create the shared library. Run 'printErrors()' to see the compilation errors.
  
  Backtrace:
      █
   1. └─bcgam::bcgam(...) testthat.R:3:0
   2.   └─bcgam:::bcgam.fit(...)
   3.     └─nimble::compileNimble(gaus)
   4.       └─project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
   5.         └─cppProj$compileFile(compileList, showCompilerOutput)
   6.           └─nimble:::compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
   7.             └─nimble:::compileStaticCode(dllName, cppName, showCompilerOutput)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘BRugs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 143-145 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.0Mb
installed size is 136.2Mb
  sub-directories of 1Mb or more:
    include  136.2Mb
Running examples in ‘biglasso-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict.biglasso
> ### Title: Model predictions based on a fitted 'biglasso' object
> ### Aliases: predict.biglasso coef.biglasso
> ### Keywords: models regression
> 
> ### ** Examples
> 
> ## Logistic regression
> data(colon)
> X <- colon$X
> y <- colon$y
> X.bm <- as.big.matrix(X, backingfile = "")
> fit <- biglasso(X.bm, y, penalty = 'lasso', family = "binomial")
Error in structure(new.time - time, class = "proc_time") : 
  R_Reprotect: only -14 protected items, can't reprotect index -16
Calls: biglasso -> system.time -> structure
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘methodology.Rmd’

SUMMARY: processing the following file failed:
  ‘analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘BigQuic-Ex.R’ failed
The error most likely occurred in:

> ### Name: BigQuic
> ### Title: Big Quadratic Inverse Covariance Estimation
> ### Aliases: BigQuic
> ### Keywords: BigQUIC package covariance regularization graphical model
> ###   lasso Newton coordinate descent
> 
> ### ** Examples
> 
> lambda <- 0.91
> exampleResult <- BigQuic(inputFileName = paste(path.package("BigQuic"), 
+                          "/extdata/testInput", sep = ""), 
+                          outputFileName = tempfile(pattern = 
+                          "BigQuic_output_matrix", fileext = ".Bmat"),
+                          lambda = lambda, numthreads = 1, memory_size = 512, 
+                          seed = 1, use_ram = TRUE)

 *** caught segfault ***
address 2, cause 'memory not mapped'
Running examples in ‘bigsnpr-Ex.R’ failed
The error most likely occurred in:

> ### Name: snp_fastImputeSimple
> ### Title: Fast imputation
> ### Aliases: snp_fastImputeSimple
> 
> ### ** Examples
> 
> bigsnp <- snp_attachExtdata("example-missing.bed")
> G <- bigsnp$genotypes
> G[, 2]  # some missing values
  [1] NA NA  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  1  0  1  0
 [26]  0  0  0  0  1  0  1  0  0  0  0  1  0  1  0  0  0  0  0  0  0  0  0  1  0
 [51]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
 [76]  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0 NA
[101]  0  1  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0 NA  0  0  0  0  0
[126]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0 NA  0
[151]  1  0  0  0  0  0  0  0  0  0  0 NA  0  0  0  0  0  0  0  0  0  0  1  0  0
[176]  0  0  0  0  0  0 NA  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  1  0  0
> G2 <- snp_fastImputeSimple(G)

 *** caught segfault ***
address f8252000, cause 'invalid permissions'

Traceback:
 1: impute(Gna, method, ncores)
 2: snp_fastImputeSimple(G)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘bigstatsr-Ex.R’ failed
The error most likely occurred in:

> ### Name: asPlotlyText
> ### Title: Plotly text
> ### Aliases: asPlotlyText
> 
> ### ** Examples
> 
> set.seed(1)
> 
> X <- big_attachExtdata()
> svd <- big_SVD(X, big_scale(), k = 10)

 *** caught segfault ***
address f8008000, cause 'invalid permissions'

Traceback:
 1: increment_scaled_tcrossprod(K, X_part_temp, X, ind.row, ind.col.ind,     ms$center, ms$scale)
 2: big_tcrossprodSelf(X, fun.scaling = fun.scaling, ind.row = ind.row,     ind.col = ind.col, block.size = block.size)
 3: DualBigPCA(X, fun.scaling, ind.row, ind.col, block.size, k)
 4: big_SVD(X, big_scale(), k = 10)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘BioCircos.Rmd’

SUMMARY: processing the following file failed:
  ‘BioCircos.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.4Mb
    extdata   1.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running examples in ‘birdring-Ex.R’ failed
The error most likely occurred in:

> ### Name: draw.recmap
> ### Title: Plot ringing data
> ### Aliases: draw.recmap
> ### Keywords: graphics
> 
> ### ** Examples
> 
> data(lancol)
> if (requireNamespace("rgeos", quietly=TRUE) && packageVersion("rgeos") >= "0.5.1") {
+   if (rgeos::get_RGEOS_CheckValidity() == 1L) rgeos::set_RGEOS_CheckValidity(2L)
+ }
> draw.recmap(lancol,lines=2,border='gray',subset="ring=='13B...6919'",gcircle=TRUE,zoom=3)
Error in RGEOSBinTopoFunc(spgeom1, spgeom2, byid, id, drop_lower_td, unaryUnion_if_byid_false,  : 
  TopologyException: Input geom 0 is invalid: Ring Self-intersection at or near point 23.325118450000002 43.886598820000003 at 23.325118450000002 43.886598820000003
Calls: draw.recmap -> lapply -> FUN -> gIntersection -> RGEOSBinTopoFunc
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
Package suggested but not available for checking: ‘IHW’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   7.9Mb
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE.FC
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE.FC REGE.FC.ow REGE REGE.ow REGE.for REGD.for REGE.ow.for
> ###   REGD.ow.for REGE.ownm.for REGE.ownm.diag.for REGE.nm.for
> ###   REGE.nm.diag.for REGE.ne.for REGE.ow.ne.for REGE.ownm.ne.for
> ###   REGE.nm.ne.for REGD.ne.for REGD.ow.ne.for
> ### Keywords: cluster graphs
> 
> ### ** Examples
> 
> n <- 20
> net <- matrix(NA, ncol = n, nrow = n)
> clu <- rep(1:2, times = c(5, 15))
> tclu <- table(clu)
> net[clu == 1, clu == 1] <- 0
> net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1) * sample(c(0, 1),
+    size = tclu[1] * tclu[2], replace = TRUE, prob = c(3/5, 2/5))
> net[clu == 2, clu == 1] <- 0
> net[clu == 2, clu == 2] <- 0
> 
> D <- REGE.for(M = net)$E # Any other REGE function can be used
> plot.mat(net, clu = cutree(hclust(d = as.dist(1 - D), method = "ward.D"),
+    k = 2))
> # REGE returns similarities, which have to be converted to
> # disimilarities
> 
> res <- optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss", blocks = "reg")


Starting optimization of the partiton 1 of 10 partitions.
Starting partition: 1 2 1 1 1 1 1 1 1 2 2 1 2 2 2 2 2 1 1 1 

 *** caught segfault ***
address 6383f964, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, approaches = approaches, blocks = blocks,     useMulti = useMulti, save.initial.param = save.initial.param.opt,     ...)
 2: optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss",     blocks = "reg")
An irrecoverable exception occurred. R is aborting now ...
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BoolNet_package_vignette.Snw.Rnw’ using Sweave

Error: processing vignette 'BoolNet_package_vignette.Snw.Rnw' failed with diagnostics:
 chunk 13 
Error in net$interactions[[idx]][[functionIndices[idx]]] : 
  subscript out of bounds

--- failed re-building ‘BoolNet_package_vignette.Snw.Rnw’

SUMMARY: processing the following file failed:
  ‘BoolNet_package_vignette.Snw.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   2.8Mb
Packages suggested but not available for checking: 'glmmADMB', 'glmmTMB'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   7.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    fonts   2.4Mb
    lib     3.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'c3'

The following objects are masked from 'package:graphics':

    grid, legend

Quitting from lines 53-62 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘examples.Rmd’

SUMMARY: processing the following file failed:
  ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc        4.2Mb
    pictures   3.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc           1.0Mb
    htmlwidgets   3.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   1.6Mb
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    doc  37.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘catmaply.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 111-117 (catmaply.Rmd) 
Error: processing vignette 'catmaply.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘catmaply.Rmd’

SUMMARY: processing the following file failed:
  ‘catmaply.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
Running examples in ‘CEDARS-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_project
> ### Title: Create a New CEDARS Project
> ### Aliases: create_project
> 
> ### ** Examples
> 
> # The code below creates an instance of CEDARS project on a public test MongoDB cluster, populated
> # with fictitious EHR corpora.
> 
> # MongoDB credentials
> db_user_name <- "testUser"
> db_user_pw <- "testPW"
> db_host <- "cedars.yvjp6.mongodb.net"
> db_port <- NA
> 
> # Using standard MongoDB URL format
> uri_fun <- mongo_uri_standard
> 
> # Name for MongoDB database which will contain the CEDARS project
> # In this case we generate a random name
> mongo_database <- find_project_name()
Error: No suitable servers found (`serverSelectionTryOnce` set): [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed calling ismaster on 'cedars-shard-00-00.yvjp6.mongodb.net:27017'] [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed calling ismaster on 'cedars-shard-00-01.yvjp6.mongodb.net:27017'] [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify faile
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    2.3Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    include  35.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.9Mb
Package suggested but not available for checking: ‘iptools’
Running ‘test-all.R’ [28s/36s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("checkmate")
  Loading required package: checkmate
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_checkNames.R:34:3): checkNames ────────────────────────────────
  testNames("ä", type = "strict") is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  ── Failure (test_checkNames.R:35:3): checkNames ────────────────────────────────
  testNames("ä", type = "ids") is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 2899 ]
  Error: Test failures
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    1.7Mb
    help   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘chromoMap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 215-217 (chromoMap.Rmd) 
Error: processing vignette 'chromoMap.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘chromoMap.Rmd’

SUMMARY: processing the following file failed:
  ‘chromoMap.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘chronicle.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: magrittr
Quitting from lines 38-67 (chronicle.Rmd) 
Error: processing vignette 'chronicle.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building ‘chronicle.Rmd’

SUMMARY: processing the following file failed:
  ‘chronicle.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    3.6Mb
    help   1.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        6.0Mb
    skeleton   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘clinDataReview-dataPreprocessing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Data annotated with variable(s): ETHNIC ('ETHNIC'), ARM ('ARM') from the 'custom' dataset based on the variable(s):	USUBJID ('USUBJID').
354 records with ARM ('ARM') %in% 'Placebo' are filtered in data.
--- finished re-building ‘clinDataReview-dataPreprocessing.Rmd’

--- re-building ‘clinDataReview-dataVisualization.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Warning: Ignoring unknown aesthetics: text
Quitting from lines 154-187 (clinDataReview-dataVisualization.Rmd) 
Error: processing vignette 'clinDataReview-dataVisualization.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘clinDataReview-dataVisualization.Rmd’

--- re-building ‘clinDataReview-reporting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘clinDataReview-reporting.Rmd’

SUMMARY: processing the following file failed:
  ‘clinDataReview-dataVisualization.Rmd’

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘RWeka’
Error(s) in re-building vignettes:
  ...
--- re-building ‘clustcurv.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 108-109 (clustcurv.Rmd) 
Error: processing vignette 'clustcurv.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘clustcurv.Rmd’

SUMMARY: processing the following file failed:
  ‘clustcurv.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_clusterR_package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 403-416 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
--- failed re-building ‘the_clusterR_package.Rmd’

SUMMARY: processing the following file failed:
  ‘the_clusterR_package.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   1.8Mb
Found the following files/directories:
  ‘fda7wnr6u.c’
Package suggested but not available for checking: ‘gifski’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
Package suggested but not available for checking: ‘rscala’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    help   1.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help          1.0Mb
    htmlwidgets   3.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   6.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs          2.6Mb
    sample_data   2.8Mb
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(coro)
  > 
  > test_check("coro")
  
  
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   3.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘covid19dbcand.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 70-71 (covid19dbcand.Rmd) 
Error: processing vignette 'covid19dbcand.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘covid19dbcand.Rmd’

SUMMARY: processing the following file failed:
  ‘covid19dbcand.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   8.0Mb
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer2’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘CPMandPERT.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 109-111 (CPMandPERT.Rmd) 
Error: processing vignette 'CPMandPERT.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘CPMandPERT.Rmd’

--- re-building ‘LESS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-64 (LESS.Rmd) 
Error: processing vignette 'LESS.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘LESS.Rmd’

SUMMARY: processing the following files failed:
  ‘CPMandPERT.Rmd’ ‘LESS.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
Running examples in ‘ctsemOMX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ctGenerateFromFit
> ### Title: Generates data according to the model estimated in a ctsemFit
> ###   object.
> ### Aliases: ctGenerateFromFit
> 
> ### ** Examples
> 
> 
> data(AnomAuth) 
> AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2), 
+   Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2)) 
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
> AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel)
wide format data detected
Running ctsemCarefulFit with 14 parameters
Running ctsem with 14 parameters

Beginning initial fit attempt
Running ctsem with 14 parameters
terminate called after throwing an instance of 'std::runtime_error'
  what():  std::bad_alloc
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.8Mb
    doc    1.1Mb
    libs   5.5Mb
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc', 'Rmosek'
Running examples in ‘CVXR-Ex.R’ failed
The error most likely occurred in:

> ### Name: diag,Expression-method
> ### Title: Matrix Diagonal
> ### Aliases: diag,Expression-method diag
> 
> ### ** Examples
> 
> C <- Variable(3,3)
> obj <- Maximize(C[1,3])
> constraints <- list(diag(C) == 1, C[1,2] == 0.6, C[2,3] == -0.3, C == Variable(3,3, PSD = TRUE))
> prob <- Problem(obj, constraints)
> result <- solve(prob)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: scs::scs(A = args$A, b = args$b, obj = args$c, cone = cones,     control = control)
 2: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 3: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 4: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 5: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 6: psolve(a, solver = NA, ...)
 7: psolve(a, solver = NA, ...)
 8: solve(prob)
 9: solve(prob)
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cycling_data_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘cycling_data_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
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    libs   6.3Mb
installed size is  5.2Mb
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installed size is  5.2Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘DA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-74 (DA.Rmd) 
Error: processing vignette 'DA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘DA.Rmd’

SUMMARY: processing the following file failed:
  ‘DA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
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    deps  11.0Mb
installed size is  9.1Mb
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    lib   8.7Mb
installed size is  7.0Mb
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installed size is  5.2Mb
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    doc       2.4Mb
    extdata   1.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
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    data   5.4Mb
File ‘dcortools/libs/dcortools.so’:
  Found ‘__assert_c99’, possibly from ‘assert’ (C)
    Objects: ‘RcppExports.o’, ‘matrix_vector_operations.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
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    sample_data   3.6Mb
installed size is  5.1Mb
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Package suggested but not available for checking: ‘XLConnect’
Error(s) in re-building vignettes:
  ...
--- re-building ‘delayed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-98 (delayed.Rmd) 
Error: processing vignette 'delayed.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘delayed.Rmd’

SUMMARY: processing the following file failed:
  ‘delayed.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.7Mb
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installed size is  7.5Mb
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    doc       5.0Mb
    extdata   2.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.0Mb
    help   1.6Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'Rsymphony'
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc           9.9Mb
    htmlwidgets   3.2Mb
installed size is 11.0Mb
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installed size is  6.7Mb
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installed size is  6.7Mb
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installed size is  5.9Mb
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    R      4.0Mb
    help   1.3Mb
Package suggested but not available for checking: ‘plumberDeploy’
installed size is 15.0Mb
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    include  14.7Mb
installed size is  5.1Mb
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installed size is  5.1Mb
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installed size is  5.4Mb
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    data   4.9Mb
installed size is  6.4Mb
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    doc   4.8Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    assets   3.4Mb
    doc      2.1Mb
installed size is  5.5Mb
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    extdata   4.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   3.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘userGuide.Rmd’

SUMMARY: processing the following file failed:
  ‘userGuide.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
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    appinformation   4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsa-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 56-57 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘dsa-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘dsa-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘DSjobtracker.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'magrittr'

The following object is masked from 'package:tidyr':

    extract


Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: viridisLite
Selecting by Total
Quitting from lines 136-155 (DSjobtracker.Rmd) 
Error: processing vignette 'DSjobtracker.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘DSjobtracker.Rmd’

SUMMARY: processing the following file failed:
  ‘DSjobtracker.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 164-165 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘dub-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: DUBStepR
Attaching SeuratObject

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 63-65 (dub-vignette.Rmd) 
Error: processing vignette 'dub-vignette.Rmd' failed with diagnostics:
HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type

--- failed re-building ‘dub-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘dub-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 20.0Mb
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    libs  19.6Mb
installed size is  8.9Mb
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    data   4.3Mb
    doc    1.8Mb
    libs   2.2Mb
Running ‘testthat.R’ [515s/152s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dynutils")
  Loading required package: dynutils
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  ❌ Unable to read hdf5 files
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-h5.R:11:3): write_h5 and read_h5 works ──────────────────────────
  Error: HDF5-API Errors:
      error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  
  Backtrace:
      █
   1. └─dynutils::read_h5(file) test-h5.R:11:2
   2.   └─dynutils::read_h5_(file_h5)
   3.     └─hdf5r::h5attr(file_h5, "object_class")
   4.       └─attr_obj$read()
   5.         └─hdf5r:::H5ToR_Pre(mem_type, nelem)
  ── Error (test-h5.R:17:3): test_h5_installation works ──────────────────────────
  Error: HDF5-API Errors:
      error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  
  Backtrace:
      █
   1. ├─testthat::expect_true(test_h5_installation()) test-h5.R:17:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─dynutils::test_h5_installation()
   5.   └─dynutils:::test_h5_installation_read(detailed, file)
   6.     └─base::tryCatch(...)
   7.       └─base:::tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 546 ]
  Error: Test failures
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘gurobi’
Running examples in ‘eDMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: BacktestDMA
> ### Title: Backtest measures for Dynamic Model Averaging and comparison
> ###   with Dynamic Model Selection
> ### Aliases: BacktestDMA
> 
> ### ** Examples
> 
> 
> library(eDMA)
> 
> ## load data
> data("USData")
> 
> ## do DMA, keep the first three predictors fixed and the intercept
> Fit <- DMA(GDPDEF ~ Lag(GDPDEF, 1) + Lag(GDPDEF, 2) + Lag(GDPDEF, 3) +
+             Lag(ROUTP, 1) + Lag(UNEMP, 1), data = USData, vDelta = c(0.9, 0.95, 0.99),
+             vKeep = c(1, 2, 3))
Error in funcEstimate_Eff_par(vY, mF, vDelta, dAlpha, vKeep, dBeta, bZellnerPrior,  : 
  sort(): detected NaN
Calls: DMA -> funcEstimate_Eff_par
Execution halted
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Error(s) in re-building vignettes:
  ...
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Joining, by = "diagcode1"
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 325-330 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘EHRtemporalVariability.Rmd’

SUMMARY: processing the following file failed:
  ‘EHRtemporalVariability.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
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    xsd   4.1Mb
installed size is  7.3Mb
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    emoji_fonts   6.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    help   3.4Mb
installed size is  5.1Mb
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    data   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘epicontacts.Rmd’

--- re-building ‘epicontacts_class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
--- finished re-building ‘epicontacts_class.Rmd’

SUMMARY: processing the following file failed:
  ‘epicontacts.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   8.5Mb
Running examples in ‘EpiSignalDetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: runEpiSDReport
> ### Title: Run the EpiSignalDetection report (HTML markdown)
> ### Aliases: runEpiSDReport
> 
> ### ** Examples
> 
> #---> OR
> 
> #-- First setting the parameters to run the report for
> input <- list(
+ disease = "Salmonellosis",
+ country = "Portugal",
+ indicator = "Reported cases",
+ stratification = "Confirmed cases",
+ unit = "Month",
+ daterange = c("2011-01-01", "2016-12-31"),
+ algo = "FarringtonFlexible",
+ testingperiod = 6
+ )
> 
> #-- Second running the report based on the EpiSignalDetection::SignalData dataset
> #-- and store it in a temporary folder
> runEpiSDReport(input = input)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Package suggested but not available for checking: ‘mzR’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    2.1Mb
    libs   1.0Mb
installed size is 14.1Mb
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    doc  13.4Mb
installed size is  5.0Mb
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    extdata   1.7Mb
    shiny     2.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘estudy2-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.

Warning: CS.PA contains missing values. Some functions will not work if objects contain missing values in the middle of the series. Consider using na.omit(), na.approx(), na.fill(), etc to remove or replace them.
Warning: G.MI contains missing values. Some functions will not work if objects contain missing values in the middle of the series. Consider using na.omit(), na.approx(), na.fill(), etc to remove or replace them.
Warning: RSA.L download failed; trying again.
Quitting from lines 56-64 (estudy2-intro.Rmd) 
Error: processing vignette 'estudy2-intro.Rmd' failed with diagnostics:
Unable to import "RSA.L".
argument "conn" is missing, with no default
--- failed re-building ‘estudy2-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘estudy2-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘corehunter’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
Running examples in ‘ExhaustiveSearch-Ex.R’ failed
The error most likely occurred in:

> ### Name: ExhaustiveSearch
> ### Title: Exhaustive feature selection
> ### Aliases: ExhaustiveSearch
> 
> ### ** Examples
> 
> ## Linear Regression on mtcars data
> data(mtcars)
> 
> ##  Exhaustive search of 1023 models compared by AIC
> ES <- ExhaustiveSearch(mpg ~ ., data = mtcars, family = "gaussian",
+   performanceMeasure = "AIC")

Starting the exhaustive evaluation.

 Runtime          |  Completed  |  Status
------------------------------------------

 *** caught segfault ***
address 6666666e, cause 'memory not mapped'
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    exiftool  15.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro-faq.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (Intro-faq.Rmd) 
Error: processing vignette 'Intro-faq.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Intro-faq.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro-faq.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.8Mb
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    help   1.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Running ‘testthat.R’ [216s/265s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FCVAR)
  > 
  > test_check("FCVAR")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_post.R:67:3): Bootstrap hypothesis testing results and output are correct ──
  `FCVARboot_stats_test` not equal to `FCVARboot_stats`.
  Component "LRbs": Mean relative difference: 4.426738e-08
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘seasonal’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data-Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dm'

The following object is masked from 'package:stats':

    filter

Quitting from lines 36-39 (Data-Model.Rmd) 
Error: processing vignette 'Data-Model.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Data-Model.Rmd’

--- re-building ‘fishdata-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

`summarise()` has grouped output by 'site'. You can override using the `.groups` argument.
--- finished re-building ‘fishdata-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘Data-Model.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_fishflux.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 81-123 (intro_to_fishflux.Rmd) 
Error: processing vignette 'intro_to_fishflux.Rmd' failed with diagnostics:
Please install either RStudio or Pandoc (https://pandoc.org)
--- failed re-building ‘intro_to_fishflux.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_to_fishflux.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   4.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbit_viz.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 157-173 (fitbit_viz.Rmd) 
Error: processing vignette 'fitbit_viz.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘fitbit_viz.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbit_viz.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   3.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro-flashCard.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-32 (Intro-flashCard.Rmd) 
Error: processing vignette 'Intro-flashCard.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Intro-flashCard.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro-flashCard.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘multipanelfigure’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   8.0Mb
Running examples in ‘float-Ex.R’ failed
The error most likely occurred in:

> ### Name: eigen
> ### Title: eigen
> ### Aliases: eigen eigen,float32-method
> 
> ### ** Examples
> 
> library(float)
> 
> s = flrunif(10, 3)
> cp = crossprod(s)
> 
> eigen(cp)
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'Rsymphony'
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   2.2Mb
    libs   6.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   5.0Mb
    doc    1.7Mb
    help   1.5Mb
    libs   1.1Mb
Packages suggested but not available for checking: 'foba', 'rrlda', 'RWeka'
Packages suggested but not available for checking: 'RWeka', 'FSelector'
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > # required packages
  > library(testthat)
  > library(fst)
  > 
  > # some helper functions
  > source("testthat/helper_fstwrite.R")  # cross-version testing
  > 
  > # run tests
  > test_check("fst")
  
   *** caught segfault ***
  address 50564a3f, cause 'memory not mapped'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘futureheatwaves.Rmd’

--- re-building ‘starting_from_netcdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘starting_from_netcdf.Rmd’

SUMMARY: processing the following file failed:
  ‘futureheatwaves.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc  10.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘galah.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘galah.Rmd’

--- re-building ‘international_atlases.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘international_atlases.Rmd’

--- re-building ‘taxonomic_information.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 63-73 (taxonomic_information.Rmd) 
Error: processing vignette 'taxonomic_information.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘taxonomic_information.Rmd’

SUMMARY: processing the following file failed:
  ‘taxonomic_information.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GALLO.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 45-59 (GALLO.Rmd) 
Error: processing vignette 'GALLO.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘GALLO.Rmd’

SUMMARY: processing the following file failed:
  ‘GALLO.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 45.5Mb
  sub-directories of 1Mb or more:
    doc  44.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      2.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

SUMMARY: processing the following file failed:
  ‘gcbd.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    L8NY18   2.1Mb
    doc      1.1Mb
    libs     2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.4Mb
Package suggested but not available for checking: ‘mlpack’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   5.5Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R         9.1Mb
    extdata   1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Packages suggested but not available for checking: 'av', 'gifski'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggBubbles.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 30-40 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
could not find function "CRANpkg"
--- failed re-building ‘ggBubbles.Rmd’

SUMMARY: processing the following file failed:
  ‘ggBubbles.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
`geom_smooth()` using formula 'y ~ x'
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

The following objects are masked from 'package:moonBook':

    addLabelDf, getMapping

Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   2.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.2Mb
    testdata   5.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix
Quitting from lines 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fully-customed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘fully-customed.Rmd’

--- re-building ‘using-ggVennDiagram.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 73-81 (using-ggVennDiagram.Rmd) 
Error: processing vignette 'using-ggVennDiagram.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘using-ggVennDiagram.Rmd’

--- re-building ‘using-new-shapes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘using-new-shapes.Rmd’

--- re-building ‘venn-plot-with-more-than-four-sets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘venn-plot-with-more-than-four-sets.Rmd’

SUMMARY: processing the following file failed:
  ‘using-ggVennDiagram.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs            1.9Mb
    test_data       2.2Mb
    vignette_data   1.3Mb
Running examples in ‘glmmTMB-Ex.R’ failed
The error most likely occurred in:

> ### Name: VarCorr.glmmTMB
> ### Title: Extract variance and correlation components
> ### Aliases: VarCorr.glmmTMB VarCorr
> ### Keywords: internal
> 
> ### ** Examples
> 
> ## Comparing variance-covariance matrix with manual computation
> data("sleepstudy",package="lme4")
> fm4 <- glmmTMB(Reaction ~ Days + (Days|Subject), sleepstudy)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: retape(set.defaults = TRUE)
 2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg,     profile = NULL, silent = !verbose, DLL = "glmmTMB")
 3: eval(substitute(expr), data, enclos = parent.frame())
 4: eval(substitute(expr), data, enclos = parent.frame())
 5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 7: fitTMB(TMBStruc)
 8: glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 9665a274, cause 'memory not mapped'

Traceback:
 1: retape(set.defaults = TRUE)
 2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg,     profile = NULL, silent = !verbose, DLL = "glmmTMB")
 3: eval(substitute(expr), data, enclos = parent.frame())
 4: eval(substitute(expr), data, enclos = parent.frame())
 5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 7: fitTMB(TMBStruc)
 8: glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: cox.path
> ### Title: Fit a Cox regression model with elastic net regularization for a
> ###   path of lambda values
> ### Aliases: cox.path
> 
> ### ** Examples
> 
> set.seed(2)
> nobs <- 100; nvars <- 15
> xvec <- rnorm(nobs * nvars)
> xvec[sample.int(nobs * nvars, size = 0.4 * nobs * nvars)] <- 0
> x <- matrix(xvec, nrow = nobs)
> beta <- rnorm(nvars / 3)
> fx <- x[, seq(nvars / 3)] %*% beta / 3
> ty <- rexp(nobs, exp(fx))
> tcens <- rbinom(n = nobs, prob = 0.3, size = 1)
> jsurv <- survival::Surv(ty, tcens)
> fit1 <- glmnet:::cox.path(x, jsurv)
> 
> # works with sparse x matrix
> x_sparse <- Matrix::Matrix(x, sparse = TRUE)
> fit2 <- glmnet:::cox.path(x_sparse, jsurv)
Error in elnet.fit(x, z, w, lambda, alpha, intercept = FALSE, thresh = thresh,  : 
  NA/NaN/Inf in foreign function call (arg 23)
Calls: <Anonymous> -> cox.fit -> elnet.fit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Coxnet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

(process:20801): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 9'

(process:20801): Pango-WARNING **: font_face status is: <unknown error status>

(process:20801): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:20801): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 9', text='m'
Quitting from lines 191-193 (Coxnet.Rmd) 
Error: processing vignette 'Coxnet.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 19)
--- failed re-building ‘Coxnet.Rmd’

--- re-building ‘glmnet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loaded lars 1.2

--- finished re-building ‘glmnet.Rmd’

--- re-building ‘glmnetFamily.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loaded glmnet 4.1-2
Quitting from lines 86-89 (glmnetFamily.Rmd) 
Error: processing vignette 'glmnetFamily.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 25)
--- failed re-building ‘glmnetFamily.Rmd’

--- re-building ‘relax.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘relax.Rmd’

SUMMARY: processing the following files failed:
  ‘Coxnet.Rmd’ ‘glmnetFamily.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Running ‘testthat.R’ [21s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GpGp)
  > 
  > test_check("GpGp")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_loglik.R:33:5): likelihood approximations are exact when m = n-1 ──
  llobj$loglik not equal to `ll_exact`.
  1/1 mismatches
  [1] 217 - 62.7 == 155
  ── Failure (test_loglik.R:39:5): likelihood approximations are exact when m = n-1 ──
  llobj$loglik not equal to `ll_exact`.
  1/1 mismatches
  [1] 217 - 62.7 == 155
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 117 ]
  Error: Test failures
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gprofiler2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 243-244 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘gprofiler2.Rmd’

SUMMARY: processing the following file failed:
  ‘gprofiler2.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    help   4.5Mb
Packages required but not available: 'seasonal', 'x13binary'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.6Mb
installed size is 169.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    java  166.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    HaDeX   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘staplr’
Installation failed.
See ‘/home/ripley/R/packages/tests32/handwriter.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_use.Rmd’

SUMMARY: processing the following file failed:
  ‘Basic_use.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc           2.8Mb
    htmlwidgets   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hchinamap.Rmd’

SUMMARY: processing the following file failed:
  ‘hchinamap.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   1.1Mb
Running examples in ‘hdf5r-Ex.R’ failed
The error most likely occurred in:

> ### Name: H5A-class
> ### Title: Class for representing HDF5 attributes
> ### Aliases: H5A-class H5A
> 
> ### ** Examples
> 
> fname <- tempfile(fileext = ".h5")
> file <- H5File$new(fname, mode = "a")
> h5attr(file, "attr_numeric") <- rnorm(10)
> a <- file$attr_open("attr_numeric")
> a$get_info()
  corder_valid corder cset data_size
1            0      0    0        80
> a$attr_name()
[1] "attr_numeric"
> a$get_space()
Class: H5S
Type: Simple
Dims: 10
Maxdims: 10
> a$get_type()
Class: H5T_FLOAT
Datatype: H5T_IEEE_F64LE
> a$get_storage_size()
[1] 80
> a$read()
Error in H5ToR_Pre(mem_type, nelem) : HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type
Calls: <Anonymous> -> H5ToR_Pre
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdf5r.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 159-160 (hdf5r.Rmd) 
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type

--- failed re-building ‘hdf5r.Rmd’

SUMMARY: processing the following file failed:
  ‘hdf5r.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdnom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

(process:28203): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 10.5'

(process:28203): Pango-WARNING **: font_face status is: no error has occurred

(process:28203): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:28203): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 10.5', text='M'
Quitting from lines 367-379 (hdnom.Rmd) 
Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 16)
--- failed re-building ‘hdnom.Rmd’

SUMMARY: processing the following file failed:
  ‘hdnom.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 87-94 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘kmeans-umap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Using compatibility `.name_repair`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Joining, by = "service_line"
--- finished re-building ‘kmeans-umap.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.2.1

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Quitting from lines 109-111 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘heatmaply.Rmd’

SUMMARY: processing the following file failed:
  ‘heatmaply.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hermiter.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'data.table'

The following objects are masked from 'package:dplyr':

    between, first, last

Quitting from lines 542-544 (hermiter.Rmd) 
Error: processing vignette 'hermiter.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hermiter.Rmd’

SUMMARY: processing the following file failed:
  ‘hermiter.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Found the following significant warnings:
  mapping.cpp:95:58: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
See ‘/home/ripley/R/packages/tests32/hilbertSimilarity.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RProtoBuf’
Package suggested but not available for checking: ‘trackr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hpackedbubble.Rmd’

SUMMARY: processing the following file failed:
  ‘hpackedbubble.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   4.5Mb
    doc    1.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hwordcloud.Rmd’

SUMMARY: processing the following file failed:
  ‘hwordcloud.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hyperoverlap-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 51-58 (hyperoverlap-vignette.Rmd) 
Error: processing vignette 'hyperoverlap-vignette.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘hyperoverlap-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘hyperoverlap-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ibmsunburst.Rmd’

SUMMARY: processing the following file failed:
  ‘ibmsunburst.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_iBreakDown_description.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Welcome to DALEX (version: 2.3.0).
Find examples and detailed introduction at: http://ema.drwhy.ai/
Additional features will be available after installation of: ggpubr.
Use 'install_dependencies()' to get all suggested dependencies
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in randomForest.default(m, y, ...) :
  The response has five or fewer unique values.  Are you sure you want to do regression?
--- finished re-building ‘vignette_iBreakDown_description.Rmd’

--- re-building ‘vignette_iBreakDown_titanic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Welcome to DALEX (version: 2.3.0).
Find examples and detailed introduction at: http://ema.drwhy.ai/
Additional features will be available after installation of: ggpubr.
Use 'install_dependencies()' to get all suggested dependencies
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in randomForest.default(m, y, ...) :
  The response has five or fewer unique values.  Are you sure you want to do regression?
Quitting from lines 91-92 (vignette_iBreakDown_titanic.Rmd) 
Error: processing vignette 'vignette_iBreakDown_titanic.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘vignette_iBreakDown_titanic.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette_iBreakDown_titanic.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.1000genomes.hs37d5’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.7Mb
Package required but not available: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘model_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘parameter_details.Rmd’

--- re-building ‘resources.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘resources.Rmd’

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

> ### Name: ifa.bic
> ### Title: A function to compute the BIC
> ### Aliases: ifa.bic
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(memory)

 *** caught segfault ***
address a61a78f8, cause 'memory not mapped'

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   6.5Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    dlib-19.20   8.5Mb
Package suggested but not available for checking: ‘tesseract’
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       4.4Mb
    extdata   1.2Mb
    include   3.0Mb
    libs      6.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    doc    1.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.3Mb
Running ‘testthat.R’ [33m/10m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DALEX)
  Welcome to DALEX (version: 2.3.0).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  > library(ingredients)
  
  Attaching package: 'ingredients'
  
  The following object is masked from 'package:DALEX':
  
      feature_importance
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("ingredients")
  Aggregating predictions.. Progress: 98%. Estimated remaining time: 0 seconds.
  Aggregating predictions.. Progress: 93%. Estimated remaining time: 2 seconds.
Packages suggested but not available for checking: 'BGGM', 'glmmTMB'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Package suggested but not available for checking: ‘redux’
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A data.table containing NDVI samples for ten points over ten years
     (2002-2012).

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R  11.8Mb
Package suggested but not available for checking: ‘xcms’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘jaatha-evolution.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-33 (jaatha-evolution.Rmd) 
Error: processing vignette 'jaatha-evolution.Rmd' failed with diagnostics:
there is no package called 'coala'
--- failed re-building ‘jaatha-evolution.Rmd’

--- re-building ‘jaatha-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘jaatha-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘jaatha-evolution.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    dict   5.0Mb
Package suggested but not available for checking: ‘RProtoBuf’
Running examples in ‘jomo-Ex.R’ failed
The error most likely occurred in:

> ### Name: jomo.glm
> ### Title: Joint Modelling Imputation Compatible with glm Model
> ### Aliases: jomo.glm
> 
> ### ** Examples
> 
> 
>    # make sure sex is a factor:
>   
>   sldata<-within(sldata, sex<-factor(sex))
>   
>   # we define the data frame with all the variables 
>   
>   data<-sldata[,c("measure","age", "sex")]
>   
>   # And the formula of the substantive lm model 
>   # sex as an outcome only because it is the only binary variable in the dataset...
>   
>   formula<-as.formula(sex~age+measure)
>   
>   #And finally we run the imputation function:
>   
>   imp<-jomo.glm(formula,data, nburn=10, nbetween=10, nimp=2)
This function is beta software. Use carefully and please report any bug to the package mantainer

 *** caught segfault ***
address 70a, cause 'memory not mapped'
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation

Traceback:
 1: stopifnot(nrow(l1cov.prior) == ncol(l1cov.prior))
 2: jomo.glm(formula, data, nburn = 10, nbetween = 10, nimp = 2)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘general-introduction-to-justifier.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘general-introduction-to-justifier.Rmd’

--- re-building ‘justifier-in-intervention-development.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘justifier-in-intervention-development.Rmd’

--- re-building ‘justifier-in-study-design.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 268-269 (justifier-in-study-design.Rmd) 
Error: processing vignette 'justifier-in-study-design.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘justifier-in-study-design.Rmd’

SUMMARY: processing the following file failed:
  ‘justifier-in-study-design.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘awesome_table_in_html.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 635-638 (awesome_table_in_html.Rmd) 
Error: processing vignette 'awesome_table_in_html.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘awesome_table_in_html.Rmd’

--- re-building ‘awesome_table_in_pdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘awesome_table_in_pdf.Rmd’

--- re-building ‘best_practice_for_newline_in_latex_table.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘best_practice_for_newline_in_latex_table.Rmd’

--- re-building ‘legacy_features.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘legacy_features.Rmd’

--- re-building ‘use_kable_in_shiny.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘use_kable_in_shiny.Rmd’

SUMMARY: processing the following file failed:
  ‘awesome_table_in_html.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘KernelICA/libs/KernelICA.so’:
  Found ‘__assert_c99’, possibly from ‘assert’ (C)
    Objects: ‘KernelICAProblem.o’, ‘RcppExports.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘kgc-fine.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
--- failed re-building ‘kgc-fine.Rmd’

--- re-building ‘kgc-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
--- finished re-building ‘kgc-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘kgc-fine.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.4Mb
Package suggested but not available for checking: ‘Rmosek’
Package suggested but not available for checking: ‘gpg’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data             1.0Mb
    doc              1.0Mb
    shiny-landsepi   1.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.0Mb
    help   1.2Mb
Running ‘config.R’
  Running ‘testthat.R’
Running the tests in ‘tests/config.R’ failed.
Complete output:
  > mac_dir <- "~/Documents/Rtest/"
  > win_dir <- "C:/Rtest"
  > linux_dir <- "~/Documents/Rtest"
  > 
  > switch(Sys.info()['sysname'],
  +        "Darwin" = {working_dir <- mac_dir},
  +        "Windows" = {working_dir <- win_dir},
  +        "Linux" = {working_dir <- linux_dir})
  > 
  > rds_file_name <- "./ranListSmall.rds"
  > llo_file_name <- "./ranListSmall.llo"
  > repeat_time <- 20
  > original <- FALSE
  > compress <- TRUE
  > 
  > # rds_file_name <- "./ranListMid.rds"
  > # llo_file_name <- "./ranListMid.llo"
  > # repeat_time <- 20
  > # original <- FALSE
  > # compress <- TRUE
  > 
  > options(list(largeList.report.progress = FALSE))
  > 
  > if (dir.exists(working_dir)) {
  +   setwd(working_dir)
  +   if (file.exists(rds_file_name)) {
  +     library(futile.logger)
  +     ready_to_test <- TRUE
  +   } else {
  +     ready_to_test <- FALSE
  +   }
  + } else {
  +   ready_to_test <- FALSE
  + }
  Error in dir.exists(working_dir) : object 'working_dir' not found
  Execution halted
Package required but not available: ‘vapour’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    libs   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘LDATS_codebase.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘LDATS_codebase.Rmd’

--- re-building ‘paper-comparison.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-60 (paper-comparison.Rmd) 
Error: processing vignette 'paper-comparison.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘paper-comparison.Rmd’

--- re-building ‘rodents-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘rodents-example.Rmd’

SUMMARY: processing the following file failed:
  ‘paper-comparison.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘RtmpA_aq1h’
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 67-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage-leaflet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: sp
Quitting from lines 32-38 (usage-leaflet.Rmd) 
Error: processing vignette 'usage-leaflet.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘usage-leaflet.Rmd’

--- re-building ‘usage-leafletProxy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘usage-leafletProxy.Rmd’

SUMMARY: processing the following file failed:
  ‘usage-leaflet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   4.8Mb
Compilation used the following non-portable flag(s):
  ‘-mt’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    2.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘linkspotterVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘linkspotterVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R          1.8Mb
    doc        2.4Mb
    testdata   1.4Mb
Package suggested but not available for checking: ‘Rsymphony’
Error(s) in re-building vignettes:
  ...
--- re-building ‘lspline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘lspline.Rmd’

SUMMARY: processing the following file failed:
  ‘lspline.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘lvmcomp-Ex.R’ failed
The error most likely occurred in:

> ### Name: StEM_mirt
> ### Title: Stochastic EM algorithm for solving multivariate item response
> ###   theory model
> ### Aliases: StEM_mirt
> 
> ### ** Examples
> 
> # run a toy example based on the M2PL model
> 
> # load a simulated dataset
> attach(data_sim_mirt)
> 
> # generate starting values for the algorithm
> A0 <- Q
> d0 <- rep(0, J)
> theta0 <- matrix(rnorm(N*K, 0, 1),N)
> sigma0 <- diag(1, K) 
> 
> # do the confirmatory MIRT analysis
> # to enable multicore processing, set parallel = T
> mirt_res <- StEM_mirt(response, Q, A0, d0, theta0, sigma0)

Step  1	| 
Step  2	| 
Step  3	| 
Step  4	|
Running examples in ‘lvnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: lvnet
> ### Title: Confirmatory Latent Variable Network Models
> ### Aliases: lvnet
> 
> ### ** Examples
> 
> # Load dataset:
> library("lavaan")
This is lavaan 0.6-9
lavaan is FREE software! Please report any bugs.
> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # Measurement model:
> Lambda <- matrix(0, 9, 3)
> Lambda[1:3,1] <- NA
> Lambda[4:6,2] <- NA
> Lambda[7:9,3] <- NA
> 
> # Fit CFA model:
> CFA <- lvnet(Data, lambda = Lambda)
Error: C stack usage  331191444 is too close to the limit
Error: The job for model 'model' exited abnormally with the error message: User interrupt
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    TS_files     6.0Mb
    base_files   6.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(macleish)
  Loading required package: etl
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("macleish")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-macleish.R:14:3): data integrity ──────────────────────────────
  all(epsg == 4326) is not TRUE
  
  `actual`:   <NA>
  `expected`: TRUE
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 4 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'av', 'rsvg', 'tesseract', 'gifski'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 227-236 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
R: non-conforming drawing primitive definition `text' @ error/draw.c/RenderMVGContent/4372
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘latin_square.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 90-91 (latin_square.Rmd) 
Error: processing vignette 'latin_square.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘latin_square.Rmd’

--- re-building ‘make_prior.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-145 (make_prior.Rmd) 
Error: processing vignette 'make_prior.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘make_prior.Rmd’

--- re-building ‘neonatal_mortality.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘neonatal_mortality.Rmd’

--- re-building ‘wheat_breeding.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 94-95 (wheat_breeding.Rmd) 
Error: processing vignette 'wheat_breeding.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘wheat_breeding.Rmd’

SUMMARY: processing the following files failed:
  ‘latin_square.Rmd’ ‘make_prior.Rmd’ ‘wheat_breeding.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘manipulateWidgets.Rmd’

SUMMARY: processing the following file failed:
  ‘manipulateWidgets.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.2Mb
    help   1.6Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    mapdata  33.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data          1.4Mb
    doc           1.6Mb
    htmlwidgets   2.3Mb
    libs          2.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    data   2.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 114-119 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    mapdata   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Packages suggested but not available for checking: 'REBayes', 'flashr'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Running examples in ‘mdendro-Ex.R’ failed
The error most likely occurred in:

> ### Name: linkage
> ### Title: Extended Agglomerative Hierarchical Clustering
> ### Aliases: linkage descplot
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## Plot and summary of unweighted arithmetic linkage (UPGMA) dendrogram
> lnk1 <- linkage(UScitiesD)
> plot(lnk1)
> summary(lnk1)
linkage(prox = UScitiesD,
        type.prox = "distance",
        digits = 0,
        method = "arithmetic",
        weighted = FALSE,
        group = "variable")

      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")
Error in rcppLinkage(prox = prox, isDistance = (type.prox == "distance"),  : 
  std::bad_alloc
Calls: linkage -> rcppLinkage
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mdendro-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 101-104 (mdendro-vignette.Rmd) 
Error: processing vignette 'mdendro-vignette.Rmd' failed with diagnostics:
std::bad_alloc
--- failed re-building ‘mdendro-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘mdendro-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   6.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MedLEA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.3     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Loading required package: NLP

Attaching package: 'NLP'

The following object is masked from 'package:ggplot2':

    annotate

Warning in tm_map.SimpleCorpus(., stripWhitespace) :
  transformation drops documents
Quitting from lines 23-39 (MedLEA.Rmd) 
Error: processing vignette 'MedLEA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘MedLEA.Rmd’

SUMMARY: processing the following file failed:
  ‘MedLEA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    help   1.8Mb
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: BCG
> ### Title: Dataset on the Effectiveness of the BCG Vaccine for Preventing
> ###   Tuberculosis
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(BCG)
> 
> ## Univariate meta-analysis on the log of the odds ratio
> summary( meta(y=ln_OR, v=v_ln_OR, data=BCG,
+               x=cbind(scale(Latitude,scale=FALSE),
+               scale(Year,scale=FALSE))) )
Error: C stack usage  279483540 is too close to the limit
Error in running mxModel:
<simpleError: The job for model 'No predictor' exited abnormally with the error message: User interrupt>
Error: C stack usage  279483540 is too close to the limit
Error in running mxModel:
<simpleError: The job for model 'Meta analysis with ML' exited abnormally with the error message: User interrupt>
Warning: The job for model 'Meta analysis with ML' exited abnormally with the error message: User interrupt
        Length Class  Mode     
message 1      -none- character
call    0      -none- NULL     
> 
> ## Multivariate meta-analysis on the log of the odds
> ## The conditional sampling covariance is 0
> bcg <- meta(y=cbind(ln_Odd_V, ln_Odd_NV), data=BCG,
+             v=cbind(v_ln_Odd_V, cov_V_NV, v_ln_Odd_NV))
Error: C stack usage  279483540 is too close to the limit
Error in running mxModel:
<simpleError: The job for model 'Meta analysis with ML' exited abnormally with the error message: User interrupt>
Warning: The job for model 'Meta analysis with ML' exited abnormally with the error message: User interrupt
> summary(bcg)
        Length Class  Mode     
message 1      -none- character
call    0      -none- NULL     
> 
> plot(bcg)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    5.7Mb
    libs   1.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgcviz.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.
Loading required package: qgam
Loading required package: ggplot2
Registered S3 method overwritten by 'mgcViz':
  method from  
  +.gg   GGally

Attaching package: 'mgcViz'

The following objects are masked from 'package:stats':

    qqline, qqnorm, qqplot

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 173-181 (mgcviz.rmd) 
Error: processing vignette 'mgcviz.rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘mgcviz.rmd’

SUMMARY: processing the following file failed:
  ‘mgcviz.rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
Loading required package: Matrix
Quitting from lines 109-112 (Analysis.Rmd) 
Error: processing vignette 'Analysis.Rmd' failed with diagnostics:
objective in x0 returns NA
--- failed re-building ‘Analysis.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.

(process:17699): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 9.9599609375'

(process:17699): Pango-WARNING **: font_face status is: <unknown error status>

(process:17699): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:17699): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 9.9599609375', text='m'
Loading required package: Matrix
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Level2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
--- finished re-building ‘Level2.Rmd’

SUMMARY: processing the following file failed:
  ‘Analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'REBayes', 'Rmosek'
Installation failed.
See ‘/home/ripley/R/packages/tests32/mlpack.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘FSelector’
Packages suggested but not available for checking:
  'FSelector', 'rrlda', 'RWeka'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   2.4Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    images   1.4Mb
    shiny   15.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mnlogit.Rnw’ using Sweave
Package: mnlogit
Version: 1.2.6
Multinomial Logit Choice Models.
Scientific Computing Group, Sentrana Inc.
Loading required package: dfidx

Attaching package: 'dfidx'

The following object is masked from 'package:stats':

    filter


Attaching package: 'mlogit'

The following objects are masked from 'package:mnlogit':

    hmftest, index, scoretest

Loading required package: stats4
Loading required package: splines

Attaching package: 'VGAM'

The following objects are masked from 'package:mlogit':

    has.intercept, lrtest

The following object is masked from 'package:mnlogit':

    lrtest
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ms-perks-features.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ms-perks-features.Rmd’

--- re-building ‘ms-r-python-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ms-r-python-examples.Rmd’

--- re-building ‘ms-rmarkdown.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Welcome to DALEX (version: 2.3.0).
Find examples and detailed introduction at: http://ema.drwhy.ai/
Additional features will be available after installation of: ggpubr.
Use 'install_dependencies()' to get all suggested dependencies
`new_observation` argument is NULL. `new_observation_n` observations needed to calculate local explanations are taken from the data.

Quitting from lines 59-75 (ms-rmarkdown.Rmd) 
Error: processing vignette 'ms-rmarkdown.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ms-rmarkdown.Rmd’

SUMMARY: processing the following file failed:
  ‘ms-rmarkdown.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc  23.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘molaR_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: alphahull
Loading required package: rgl
Loading required package: Rvcg
Quitting from lines 58-60 (molaR_vignette.Rmd) 
Error: processing vignette 'molaR_vignette.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘molaR_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘molaR_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets  15.3Mb
Running examples in ‘mongolite-Ex.R’ failed
The error most likely occurred in:

> ### Name: gridfs
> ### Title: GridFS API
> ### Aliases: gridfs
> 
> ### ** Examples
> 
> # Upload a file to GridFS
> fs <- gridfs(url = "mongodb+srv://readwrite:test@cluster0-84vdt.mongodb.net/test")
Error: No suitable servers found (`serverSelectionTryOnce` set): [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed calling ismaster on 'cluster0-shard-00-01-84vdt.mongodb.net:27017'] [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed calling ismaster on 'cluster0-shard-00-02-84vdt.mongodb.net:27017'] [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify f
Execution halted
Running examples in ‘monoreg-Ex.R’ failed
The error most likely occurred in:

> ### Name: monoreg
> ### Title: Bayesian monotonic regression
> ### Aliases: monoreg
> 
> ### ** Examples
> 
> library(monoreg)
> set.seed(1)
> # nobs <- 1000
> nobs <- 50
> sigma <- 0.01
> x1 <- runif(nobs)
> x2 <- runif(nobs)
> 
> # 6 different monotonic regression surfaces:
> # mu <- sqrt(x1)
> mu <- 0.5 * x1 + 0.5 * x2
> # mu <- pmin(x1, x2)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (x1 + x2 > 1.0)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (pmax(x1, x2) > 0.5)
> # mu <- ifelse((x1 - 1.0)^2 + (x2 - 1.0)^2 < 1.0, sqrt(1.0 - (x1 - 1.0)^2 - (x2 - 1.0)^2), 0.0)
> 
> y <- rnorm(nobs, mu, sigma)
> 
> # results <- monoreg(niter=15000, burnin=5000, adapt=5000, refresh=10, 
> results <- monoreg(niter=5000, burnin=2500, adapt=2500, refresh=10, 
+                    thin=5, birthdeath=10, seed=1, rhoa=0.1, rhob=0.1, 
+                    deltai=0.1, drange=2.0, predict=rep(1.0, nobs), 
+                    include=rep(1.0, nobs), response=y, offset=NULL, 
+                    axes=cbind(x1,x2), covariates=rep(1.0, nobs), 
+                    settozero=getcmat(2), package=rep(1,3)) 
Point process configuration:
1 0 1 
1 1 0 
1 0 0 
     
Packages:
1 
0 
Starting Gibbs sampler:

 *** caught segfault ***
address 6, cause 'memory not mapped'

Traceback:
 1: monoreg(niter = 5000, burnin = 2500, adapt = 2500, refresh = 10,     thin = 5, birthdeath = 10, seed = 1, rhoa = 0.1, rhob = 0.1,     deltai = 0.1, drange = 2, predict = rep(1, nobs), include = rep(1,         nobs), response = y, offset = NULL, axes = cbind(x1,         x2), covariates = rep(1, nobs), settozero = getcmat(2),     package = rep(1, 3))
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsageOfMrSGUIDE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 119-120 (UsageOfMrSGUIDE.Rmd) 
Error: processing vignette 'UsageOfMrSGUIDE.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘UsageOfMrSGUIDE.Rmd’

SUMMARY: processing the following file failed:
  ‘UsageOfMrSGUIDE.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘msaR.Rmd’

SUMMARY: processing the following file failed:
  ‘msaR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 101-103 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘msir.Rmd’

SUMMARY: processing the following file failed:
  ‘msir.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    www   4.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘leukemiasEset’
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs   6.8Mb
Running examples in ‘mxmmod-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxMmodModel
> ### Title: Create an MMOD
> ### Aliases: mxMmodModel
> 
> ### ** Examples
> 
> data(nlsy97depression)
> # Fit one factor MMOD
> structure <- list(
+   F1 = c('nervous', 'down', 'depressed', 'calm', 'happy')
+ )
> mmod_model <- mxMmodModel(data=nlsy97depression,
+                           modelName='1 Factor MMOD',
+                           idvar='pid', timevar='occasion', structure=structure)
Warning in mxMmodModel(data = nlsy97depression, modelName = "1 Factor MMOD",  :
  Missing values detected; omitting them.
> mmod_fit <- OpenMx::mxRun(mmod_model)
Running 1 Factor MMOD with 33 parameters
Error: C stack usage  271684756 is too close to the limit
Error: The job for model '1 Factor MMOD' exited abnormally with the error message: User interrupt
Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
Running examples in ‘NADIA-Ex.R’ failed
The error most likely occurred in:

> ### Name: PipeOpSample_B
> ### Title: PipeOpSample_B
> ### Aliases: PipeOpSample_B
> 
> ### ** Examples
> 
> {
+   graph <- PipeOpSample_B$new() %>>% mlr3learners::LearnerClassifGlmnet$new()
+   graph_learner <- GraphLearner$new(graph)
+ 
+   # Task with NA
+   set.seed(1)
+   resample(tsk("pima"), graph_learner, rsmp("cv", folds = 3))
+ }
INFO  [22:26:22.106] [mlr3]  Applying learner 'impute_sample_B.classif.glmnet' on task 'pima' (iter 2/3) 
Error in approx(lambda, seq(lambda), sfrac) : 
  need at least two non-NA values to interpolate
Calls: resample ... resolve.list -> signalConditionsASAP -> signalConditions
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Errors_Statistic_and_Handling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Errors_Statistic_and_Handling.Rmd’

--- re-building ‘NADIA_examples_and_motivation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 138-156 (NADIA_examples_and_motivation.Rmd) 
Error: processing vignette 'NADIA_examples_and_motivation.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘NADIA_examples_and_motivation.Rmd’

SUMMARY: processing the following file failed:
  ‘NADIA_examples_and_motivation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 16.4Mb
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    extdata  16.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data     2.0Mb
    libs     1.9Mb
    models   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Installation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Installation.Rmd’

--- re-building ‘neurons-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: rgl
Registered S3 method overwritten by 'nat':
  method             from
  as.mesh3d.ashape3d rgl 
Some nat functions depend on a CMTK installation. See ?cmtk and README.md for details.

Attaching package: 'nat'

The following objects are masked from 'package:base':

    intersect, setdiff, union

Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 413-417 (neurons-intro.Rmd) 
Error: processing vignette 'neurons-intro.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘neurons-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘neurons-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘natstrat.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 71-81 (natstrat.Rmd) 
Error: processing vignette 'natstrat.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘natstrat.Rmd’

SUMMARY: processing the following file failed:
  ‘natstrat.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.8Mb
installed size is  9.6Mb
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    data   9.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Running examples in ‘NCutYX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ancut
> ### Title: Cluster the Columns of Y into K Groups with the Help of External
> ###   Features X.
> ### Aliases: ancut
> 
> ### ** Examples
> 
> #This sets up the initial parameters for the simulation.
> library(MASS)#for mvrnorm
> library(fields)
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.7-0 (2021-06-25) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

The following objects are masked from ‘package:base’:

    backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
> n=30 #Sample size
> B=50 #Number of iterations in the simulated annealing algorithm.
> L=10000 #Temperature coefficient.
> p=50 #Number of columns of Y.
> q=p #Number of columns of X.
> h1=0.15
> h2=0.25
> 
> S=matrix(0.2,q,q)
> S[1:(q/2),(q/2+1):q]=0
> S[(q/2+1):q,1:(q/2)]=0
> S=S-diag(diag(S))+diag(q)
> 
> mu=rep(0,q)
> 
> W0=matrix(1,p,p)
> W0[1:(p/2),1:(p/2)]=0
> W0[(p/2+1):p,(p/2+1):p]=0
> Denum=sum(W0)
> 
> B2=matrix(0,q,p)
> for (i in 1:(p/2)){
+    B2[1:(q/2),i]=runif(q/2,h1,h2)
+    in1=sample.int(q/2,6)
+    B2[-in1,i]=0
+ }
> 
> for (i in (p/2+1):p){
+    B2[(q/2+1):q,i]=runif(q/2,h1,h2)
+    in2=sample(seq(q/2+1,q),6)
+    B2[-in2,i]=0
+ }
> 
> X=mvrnorm(n, mu, S)
> Z=X%*%B2
> Y=Z+matrix(rnorm(n*p,0,1),n,p)
> #Our method
> Res=ancut(Y=Y,X=X,B=B,L=L,alpha=0,ncv=3)
Error in if (J2 > J) { : missing value where TRUE/FALSE needed
Calls: ancut
Execution halted
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of ‘Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests32/NestedCategBayesImpute.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NetRep)
  > 
  > test_check("NetRep")
  
   *** caught segfault ***
  address eeb4e379, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘NetRep.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

 *** caught segfault ***
address aa419af7, cause 'memory not mapped'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introducing_nhanesA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 74-75 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
Timeout was reached: [wwwn.cdc.gov] Resolving timed out after 10000 milliseconds
--- failed re-building ‘Introducing_nhanesA.Rmd’

SUMMARY: processing the following file failed:
  ‘Introducing_nhanesA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   7.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_nimbleEcology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 156-160 (Introduction_to_nimbleEcology.Rmd) 
Error: processing vignette 'Introduction_to_nimbleEcology.Rmd' failed with diagnostics:
Failed to create the shared library. Run 'printErrors()' to see the compilation errors.

--- failed re-building ‘Introduction_to_nimbleEcology.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_to_nimbleEcology.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    CppCode  10.9Mb
    R         6.1Mb
    include   5.4Mb
    libs      3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘geocode.Rmd’

SUMMARY: processing the following file failed:
  ‘geocode.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    examples   7.2Mb
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: NMFfitX-class
> ### Title: Virtual Class to Handle Results from Multiple Runs of NMF
> ###   Algorithms
> ### Aliases: NMFfitX-class
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 20; counts <- c(5, 2, 3);
> V <- syntheticNMF(n, counts)
> 
> # perform multiple runs of one algorithm (default is to keep only best fit)
> res <- nmf(V, 3, nrun=3)
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL,  : 
  Error: memory could not be allocated for instance of type big.matrix
Calls: nmf ... gVariable -> <Anonymous> -> <Anonymous> -> big.matrix
Timing stopped at: 0.03 0.037 0.069
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R            1.7Mb
    test_files   4.4Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    2.3Mb
    help   3.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/ondisc.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'RMark', 'R2ucare'
Error(s) in re-building vignettes:
  ...
--- re-building ‘openland_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
Content type 'application/octet-stream' length 5309066 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

Quitting from lines 264-269 (openland_vignette.Rmd) 
Error: processing vignette 'openland_vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘openland_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘openland_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘umx’
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R        2.8Mb
    data     1.0Mb
    libs     4.3Mb
    models   4.5Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxModelAverage
> ### Title: Information-Theoretic Model-Averaging and Multimodel Inference
> ### Aliases: mxModelAverage omxAkaikeWeights omxAICWeights
> 
> ### ** Examples
> 
> require(OpenMx)
> data(demoOneFactor)
> factorModel1 <- mxModel(
+ 	"OneFactor1",
+ 	mxMatrix(
+ 		"Full", 5, 1, values=0.8, 
+ 		labels=paste("a",1:5,sep=""),
+ 		free=TRUE, name="A"),
+ 	mxMatrix(
+ 		"Full", 5, 1, values=1,
+ 		labels=paste("u",1:5,sep=""),
+ 		free=TRUE, name="Udiag"),
+ 	mxMatrix(
+ 		"Symm", 1, 1, values=1,
+ 		free=FALSE, name="L"),
+ 	mxAlgebra(vec2diag(Udiag),name="U"),
+ 	mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+ 	mxExpectationNormal(
+ 		covariance = "R",
+ 		dimnames = names(demoOneFactor)),
+ 	mxFitFunctionML(),
+ 	mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorFit1 <- mxRun(factorModel1)
Running OneFactor1 with 10 parameters
Error: C stack usage  271815828 is too close to the limit
Error: The job for model 'OneFactor1' exited abnormally with the error message: User interrupt
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Package suggested but not available for checking: ‘RcppSimdJson’
Packages suggested but not available for checking:
  'gurobi', 'Rsymphony', 'lpsymphony'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         2.1Mb
    shiny-app   1.0Mb
Running ‘exporting-methods.R’
  Running ‘testthat.R’ [52s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.match_on.R:591:5): standardization_scale with svyglm ────────────
  Error: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   └─optmatch:::standardizer(des_t)
   3.     ├─stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     └─survey:::update.survey.design(...)
   5.       └─base::eval(dots[[j]], object$variables, parent.frame())
   6.         └─base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc   8.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-31 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘basic-usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 204-226 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘progressive_packing.Rmd’

SUMMARY: processing the following file failed:
  ‘progressive_packing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    9.4Mb
    libs   3.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PandemicLP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 28-30 (PandemicLP.Rmd) 
Error: processing vignette 'PandemicLP.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PandemicLP.Rmd’

--- re-building ‘PandemicLP_SumRegions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP_SumRegions.rda'
Content type 'application/octet-stream' length 13851069 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP_SumRegions.rda'
Content type 'application/octet-stream' length 13851069 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

Quitting from lines 172-175 (PandemicLP_SumRegions.Rmd) 
Error: processing vignette 'PandemicLP_SumRegions.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PandemicLP_SumRegions.Rmd’

SUMMARY: processing the following files failed:
  ‘PandemicLP.Rmd’ ‘PandemicLP_SumRegions.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parallelplot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-26 (introduction-to-parallelplot.Rmd) 
Error: processing vignette 'introduction-to-parallelplot.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction-to-parallelplot.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-parallelplot.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'glmmTMB', 'M3C'
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction-to-parcoords-.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-parcoords-.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    lib   4.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.1Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   8.6Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc   8.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘pdxTrees-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

`curl` package not installed, falling back to using `url()`
`curl` package not installed, falling back to using `url()`
Quitting from lines 93-133 (pdxTrees-vignette.Rmd) 
Error: processing vignette 'pdxTrees-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘pdxTrees-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘pdxTrees-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    help   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   1.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    help   1.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_Use.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_Usage.Rmd’ ‘Basic_Use.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.png’
Running examples in ‘PLNmodels-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.PLNmixturefit
> ### Title: Mixture visualization of a 'PLNmixturefit' object
> ### Aliases: plot.PLNmixturefit
> 
> ### ** Examples
> 
> data(trichoptera)
> trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
> myPLN <- PLNmixture(Abundance ~ 1 + offset(log(Offset)),
+            data = trichoptera, control_main = list(iterates = 0))  %>% getBestModel()

 Initialization...

 Adjusting 5 PLN mixture models.
	number of cluster = 1 
	number of cluster = 2 
	number of cluster = 3 
	number of cluster = 4 
	number of cluster = 5 

 Smoothing PLN mixture models.

 Post-treatments
 DONE!
> plot(myPLN, "pca")
> plot(myPLN, "matrix")
Warning: Transformation introduced infinite values in discrete y-axis
Error in seq.default(min, max, by = by) : 'from' must be a finite number
Calls: plot ... <Anonymous> -> f -> <Anonymous> -> seq -> seq.default
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    htmlwidgets   3.7Mb
Running ‘spelling.R’
  Running ‘testthat.R’ [1m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plumber)
  > 
  > test_check("plumber")
  
  
  Execution halted
Running examples in ‘plumbertableau-Ex.R’ failed
The error most likely occurred in:

> ### Name: tableau_invoke
> ### Title: Programatically invoke a Tableau extension function
> ### Aliases: tableau_invoke
> 
> ### ** Examples
> 
> pr_path <- system.file("plumber/stringutils/plumber.R",
+   package = "plumbertableau")
> 
> tableau_invoke(pr_path, "/lowercase", LETTERS[1:5])
Verbose logging is off. To enable it please set the environment variable `DEBUGME` to include `plumbertableau`.




Execution halted
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plumbertableau)
  > 
  > test_check("plumbertableau")
  Verbose logging is off. To enable it please set the environment variable `DEBUGME` to include `plumbertableau`.
  
  
  Verbose logging is off. To enable it please set the environment variable `DEBUGME` to include `plumbertableau`.
  
  
  
  
  Execution halted
Running ‘testthat.R’ [48s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmultinom)
  > 
  > test_check("pmultinom")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_invertpmultinom.R:37:3): Correct behavior when target probability is 0 or 1 ──
  invert.pmultinom(...) not equal to 0.
  1/1 mismatches
  [1] 6 - 0 == 6
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1561 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘about-podr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 42-64 (about-podr.Rmd) 
Error: processing vignette 'about-podr.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘about-podr.Rmd’

SUMMARY: processing the following file failed:
  ‘about-podr.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    help   3.0Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    R      6.6Mb
    data   4.6Mb
    doc    1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    test   1.2Mb
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   5.7Mb
Running examples in ‘potential-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_matrix
> ### Title: Create a Distance Matrix Between Two Spatial Objects
> ### Aliases: create_matrix
> 
> ### ** Examples
> 
> g <- create_grid(x = n3_poly, res = 200000)
> mat <- create_matrix(x = n3_pt, y = g)
Warning in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
  GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Error in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  : 
  OGRCreateCoordinateTransformation() returned NULL: PROJ available?
Calls: create_matrix ... st_transform.sfc -> st_sfc -> structure -> CPL_transform
Execution halted
Running ‘tinytest.R’ [9s/11s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("potential")
  + }
  
  test_curv.R...................    0 tests    
  test_curv.R...................    0 tests    
  test_curv.R...................    1 tests [0;32mOK[0m 
  test_curv.R...................    2 tests [0;32mOK[0m 
  test_curv.R...................    3 tests [0;32mOK[0m 
  test_curv.R...................    3 tests [0;32mOK[0m 
  test_curv.R...................    4 tests [0;32mOK[0m 
  test_curv.R...................    5 tests [0;31m1 fails[0m 
  test_curv.R...................    5 tests [0;31m1 fails[0m 
  test_curv.R...................    6 tests [0;31m1 fails[0m Error in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  : 
    OGRCreateCoordinateTransformation() returned NULL: PROJ available?
  Calls: <Anonymous> ... st_transform.sfc -> st_sfc -> structure -> CPL_transform
  In addition: Warning message:
  In CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
    GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘potential.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Linking to GEOS 3.6.4, GDAL 2.2.4, PROJ 5.2.0
This project is in maintenance mode. 
Core functionalities of `cartography` can be found in `mapsf`.
https://riatelab.github.io/mapsf/
Warning in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
  GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Quitting from lines 214-216 (potential.Rmd) 
Error: processing vignette 'potential.Rmd' failed with diagnostics:
OGRCreateCoordinateTransformation() returned NULL: PROJ available?
--- failed re-building ‘potential.Rmd’

SUMMARY: processing the following file failed:
  ‘potential.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 130-131 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PPQplan-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘PPQplan-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: predict3d
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    shinyApp   5.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘prettyglm-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 88-90 (prettyglm-vignette.Rmd) 
Error: processing vignette 'prettyglm-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘prettyglm-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘prettyglm-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI', 'lpsymphony', 'Rsymphony'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    2.3Mb
    libs   1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in getPrisma(studyStatus) :
  prismaFormat is null so attempting to make automatic one from studyStatus
Warning in getFormatNode(prismaFormat) :
  fontSize param not passed in prismaFormat
Quitting from lines 43-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PRISMA.Rmd’

SUMMARY: processing the following file failed:
  ‘PRISMA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘exclusionflowcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘PRISMA.Rmd’ ‘exclusionflowcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc           9.0Mb
    htmlwidgets   2.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘prt.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

 *** caught segfault ***
address f606df2c, cause 'memory not mapped'
Found the following files/directories:
  ‘Rtmpf_aqOB’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R          1.3Mb
    doc        4.3Mb
    examples   2.9Mb
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(testthat))
  > suppressPackageStartupMessages(library(pulsar))
  > 
  > testthat::test_check("pulsar")
  
   *** caught segfault ***
  address 33333338, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Data_Model.Rmd’

--- re-building ‘Example_Save_Data_as_CSV.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Example_Save_Data_as_CSV.Rmd’

--- re-building ‘Maps_and_Timeseries_Plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in monitor_dailyStatistic(PacNW, FUN = mean, minHours = 20) :
  Found 2 timezones. Only 'America/Los_Angeles' will be used
--- finished re-building ‘Maps_and_Timeseries_Plots.Rmd’

--- re-building ‘NowCast.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘NowCast.Rmd’

--- re-building ‘PWFSLSmoke.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 161-162 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PWFSLSmoke.Rmd’

SUMMARY: processing the following file failed:
  ‘PWFSLSmoke.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   3.4Mb
    libs      2.2Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    contrib   3.7Mb
    doc       3.2Mb
    libs      1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Qtools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 124-146 (Qtools.Rmd) 
Error: processing vignette 'Qtools.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Qtools.Rmd’

SUMMARY: processing the following file failed:
  ‘Qtools.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘quanteda-Ex.R’ failed
The error most likely occurred in:

> ### Name: corpus-class
> ### Title: Base method extensions for corpus objects
> ### Aliases: corpus-class +.corpus c.corpus [.corpus print.summary.corpus
> ### Keywords: corpus internal
> 
> ### ** Examples
> 
> # concatenate corpus objects
> corp1 <- corpus(data_char_ukimmig2010[1:2])
> corp2 <- corpus(data_char_ukimmig2010[3:4])
> corp3 <- corpus(data_char_ukimmig2010[5:6])
> summary(c(corp1, corp2, corp3))
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.list': error in evaluating the argument 'x' in selecting a method for function 'which': Illegal argument. (U_ILLEGAL_ARGUMENT_ERROR, context=`^\p{emoji_presentation}+$`)
Calls: summary ... stri_detect_regex -> .handleSimpleError -> h -> .handleSimpleError -> h
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Package version: 3.0.0
Unicode version: 7.0
ICU version: 55.1
Parallel computing: 16 of 16 threads used.
See https://quanteda.io for tutorials and examples.
Quitting from lines 80-82 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.list': error in evaluating the argument 'x' in selecting a method for function 'which': Illegal argument. (U_ILLEGAL_ARGUMENT_ERROR, context=`^\p{emoji_presentation}+$`)
--- failed re-building ‘quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc  10.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘r3dmol.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-66 (r3dmol.Rmd) 
Error: processing vignette 'r3dmol.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘r3dmol.Rmd’

--- re-building ‘style-functions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 43-49 (style-functions.Rmd) 
Error: processing vignette 'style-functions.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘style-functions.Rmd’

SUMMARY: processing the following files failed:
  ‘r3dmol.Rmd’ ‘style-functions.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    app   6.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘a01_GettingStarted.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-78 (a01_GettingStarted.Rmd) 
Error: processing vignette 'a01_GettingStarted.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘a01_GettingStarted.Rmd’

--- re-building ‘a02_VitalRates.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a02_VitalRates.Rmd’

--- re-building ‘a03_LifeHistoryTraits.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a03_LifeHistoryTraits.Rmd’

--- re-building ‘a04_AgeFromStage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a04_AgeFromStage.Rmd’

SUMMARY: processing the following file failed:
  ‘a01_GettingStarted.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RAhrefs)
  > test_check("RAhrefs")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_auth.R:10:3): api_key param doesn't accept wrong values ───────
  `rah_auth(api_key = "stupid things", verbose = TRUE)` threw an error with unexpected message.
  Expected match: "Authorization error: HTTP status code"
  Actual message: "Timeout was reached: [apiv2.ahrefs.com] Resolving timed out after 10001 milliseconds"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_auth.R:10:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─RAhrefs::rah_auth(api_key = "stupid things", verbose = TRUE)
    7.   └─httr::GET(...)
    8.     └─httr:::request_perform(req, hu$handle$handle)
    9.       ├─httr:::request_fetch(req$output, req$url, handle)
   10.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   11.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  Error: Test failures
  Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.9Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    api           3.0Mb
    htmlwidgets   7.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘randomNames.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (randomNames.Rmd) 
Error: processing vignette 'randomNames.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘randomNames.Rmd’

SUMMARY: processing the following file failed:
  ‘randomNames.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [238s/457s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(randomsearch)
  Loading required package: ParamHelpers
  Loading required package: smoof
  Loading required package: checkmate
  > 
  > test_check("randomsearch")
  Error : [ENOENT] Failed to stat '/tmp/Rtmp1XaWUm/working_dir/RtmpT3aqNC/file393a4217c2b/2_15': no such file or directory
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_randomsearch.R:83:5): parallel randomsearch works with parallelMap ──
  Error: Errors occurred in 1 slave jobs, displaying at most 10 of them:
  
  00001: Error : [ENOENT] Failed to stat '/tmp/Rtmp1XaWUm/working_dir/RtmpT3aqNC/file393a4217c2b/2_15': no such file or directory
  
  
  Backtrace:
      █
   1. ├─randomsearch::randomsearch(...) test_randomsearch.R:83:4
   2. └─randomsearch:::randomsearch.smoof_function(...)
   3.   └─parallelMap::parallelMap(...)
   4.     └─parallelMap:::checkResultsAndStopWithErrorsMessages(res)
   5.       └─parallelMap:::stopWithJobErrorMessages(...)
   6.         └─BBmisc::stopf(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 69 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RApiDatetime.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.6Mb
    etc    2.2Mb
    po     1.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Package suggested but not available for checking: ‘av’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.7Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   2.7Mb
    po    2.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    corpora   8.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RcppCNPy-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 95-104 (RcppCNPy-intro.Rmd) 
Error: processing vignette 'RcppCNPy-intro.Rmd' failed with diagnostics:
ImportError: No module named 'numpy'

Detailed traceback:
  File "<string>", line 1, in <module>
  File "/home/ripley/R/Lib32/reticulate/python/rpytools/loader.py", line 44, in _import_hook
    level=level

--- failed re-building ‘RcppCNPy-intro.Rmd’

--- re-building ‘UsingReticulate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 84-94 (UsingReticulate.Rmd) 
Error: processing vignette 'UsingReticulate.Rmd' failed with diagnostics:
ImportError: No module named 'numpy'

Detailed traceback:
  File "/home/ripley/R/Lib32/reticulate/python/rpytools/loader.py", line 44, in _import_hook
    level=level

--- failed re-building ‘UsingReticulate.Rmd’

SUMMARY: processing the following files failed:
  ‘RcppCNPy-intro.Rmd’ ‘UsingReticulate.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppFastFloat.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   5.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    include   6.6Mb
Running ‘testthat.R’ [17s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RCSF)
  > 
  > test_check("RCSF")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-CSF.R:7:3): csf algorithm works ───────────────────────────────
  length(id_ground) %in% c(15459L, 15453L) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rdf_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘rdf_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   1.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘recexcavAAR-vignette-1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-1.Rmd’

--- re-building ‘recexcavAAR-vignette-2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-2.Rmd’

--- re-building ‘recexcavAAR-vignette-3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-3.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-3.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-3.Rmd’

SUMMARY: processing the following files failed:
  ‘recexcavAAR-vignette-1.Rmd’ ‘recexcavAAR-vignette-2.Rmd’
  ‘recexcavAAR-vignette-3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ReDaMoR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 157-163 (ReDaMoR.Rmd) 
Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ReDaMoR.Rmd’

SUMMARY: processing the following file failed:
  ‘ReDaMoR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   1.3Mb
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
Package suggested but not available for checking: ‘rsolr’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    arabb      1.0Mb
    doc        1.3Mb
    examples   2.0Mb
Running ‘testthat.R’ [19s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(retrosheet)
  
  For Retrosheet data obtained with this package:
  
  The information used here was obtained free of charge from
  and is copyrighted by Retrosheet. Interested parties may
  contact Retrosheet at "www.retrosheet.org"
  
  > 
  > test_check("retrosheet")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-rmarkdown.R:14:5): Can be used in rmarkdown ───────────────────
  `runAllChunks("test-rmarkdown.Rmd")` threw an error.
  Message: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Class:   simpleError/error/condition
  Backtrace:
      █
   1. ├─testthat::expect_error(runAllChunks("test-rmarkdown.Rmd"), NA) test-rmarkdown.R:14:4
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat:::.capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─retrosheet:::runAllChunks("test-rmarkdown.Rmd")
   7.   └─rmarkdown::render(rmd, output_file = tempR, quiet = TRUE) test-rmarkdown.R:10:8
   8.     └─rmarkdown::pandoc_available(required_pandoc, error = TRUE)
   9.       └─rmarkdown:::stop2(paste(msg, collapse = " "))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 59 ]
  Error: Test failures
  Execution halted
Running examples in ‘revgeo-Ex.R’ failed
The error most likely occurred in:

> ### Name: revgeo
> ### Title: Reverse Geocoding with the Photon Geocoder for OpenStreetMap,
> ###   Google Maps, and Bing.
> ### Aliases: revgeo
> ### Keywords: geocode reverse
> 
> ### ** Examples
> 
> revgeo(longitude=-77.0229529, latitude=38.89283435)
[1] "Getting geocode data from Photon: http://photon.komoot.de/reverse?lon=-77.0229529&lat=38.89283435"

Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following object is masked from 'package:kableExtra':

    group_rows

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 231-254 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following object is masked from 'package:kableExtra':

    group_rows

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 227-251 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    doc       2.2Mb
    extdata   2.9Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        3.5Mb
    misc       1.1Mb
    pictures   1.5Mb
Running examples in ‘rGEDI-Ex.R’ failed
The error most likely occurred in:

> ### Name: clipLevel1BGeo
> ### Title: Clip GEDI Full Waveform Geolocations by Coordinates
> ### Aliases: clipLevel1BGeo
> 
> ### ** Examples
> 
> # Specifying the path to GEDI level1B data (zip file)
> outdir = tempdir()
> level1B_fp_zip <- system.file("extdata",
+                   "GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.zip",
+                   package="rGEDI")
> 
> # Unzipping GEDI level1B data
> level1Bpath <- unzip(level1B_fp_zip,exdir = outdir)
> 
> # Reading GEDI level1B data (h5 file)
> level1b<-readLevel1B(level1Bpath=level1Bpath)
> 
> # Extracting GEDI Full Waveform Geolocations
> level1bGeo<-getLevel1BGeo(level1b)

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   2%Error in self$read_low_level(file_space = self_space_id, mem_space = mem_space_id,  : 
  HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type
Calls: getLevel1BGeo ... assign -> [ -> [.H5D -> <Anonymous> -> <Anonymous> -> .Call
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘precipitation_stochastic_generation_v7.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: copula
Loading required package: RGENERATE
Loading required package: RMAWGEN
Loading required package: chron
Loading required package: date
Loading required package: vars
Loading required package: MASS
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: urca
Loading required package: lmtest

Attaching package: 'vars'

The following object is masked from 'package:copula':

    A

Loading required package: blockmatrix
Loading required package: Matrix
Loading required package: stringr

Attaching package: 'stringr'

The following object is masked from 'package:strucchange':

    boundary


Attaching package: 'lubridate'

The following objects are masked from 'package:chron':

    days, hours, minutes, seconds, years

The following object is masked from 'package:copula':

    interval

The following objects are masked from 'package:base':

    date, intersect, setdiff, union

Quitting from lines 50-63 (precipitation_stochastic_generation_v7.Rmd) 
Error: processing vignette 'precipitation_stochastic_generation_v7.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘precipitation_stochastic_generation_v7.Rmd’

SUMMARY: processing the following file failed:
  ‘precipitation_stochastic_generation_v7.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rgeoprofile.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-142 (rgeoprofile.Rmd) 
Error: processing vignette 'rgeoprofile.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rgeoprofile.Rmd’

SUMMARY: processing the following file failed:
  ‘rgeoprofile.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc     1.8Mb
    fonts   1.6Mb
    libs    1.0Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help  10.6Mb
    libs   3.1Mb
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro_rhandsontable.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_rhandsontable.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘rhymer-Ex.R’ failed
The error most likely occurred in:

> ### Name: datamuse_api
> ### Title: Call Datamuse API and return data.
> ### Aliases: datamuse_api
> 
> ### ** Examples
> 
> datamuse_api("/words?rel_rhy=test")
Error: Datamuse API request failed [503]
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-rhymer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 37-38 (intro-to-rhymer.Rmd) 
Error: processing vignette 'intro-to-rhymer.Rmd' failed with diagnostics:
Datamuse API request failed [503]
--- failed re-building ‘intro-to-rhymer.Rmd’

SUMMARY: processing the following file failed:
  ‘intro-to-rhymer.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    extdata  25.1Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    rmd   8.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    templates   5.4Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.8Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘robin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: gprege
Loading required package: gptk
Loading required package: Matrix
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.7-0 (2021-06-25) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following object is masked from 'package:Matrix':

    det

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Loading required package: qpdf
Quitting from lines 97-98 (robin.Rmd) 
Error: processing vignette 'robin.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘robin.Rmd’

SUMMARY: processing the following file failed:
  ‘robin.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'illuminaHumanv3.db'
Running examples in ‘robust-Ex.R’ failed
The error most likely occurred in:

> ### Name: overlaidDenPlot.fdfm
> ### Title: Overlaid Density Plot
> ### Aliases: overlaidDenPlot.fdfm
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   data(los, package="robustbase")
>   los.fm <- fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"),
+                          x = los, densfun = "gamma")

 *** caught segfault ***
address 4, cause 'memory not mapped'

Traceback:
 1: Tabgamma(b1, b2, alpha1, alpha2, k, A, maxta, maxtc, maxit, til,     tol)
 2: gammaRob(x, ...)
 3: fitdstnRob(x = los, densfun = "gamma")
 4: eval(model.call, sys.parent())
 5: eval(model.call, sys.parent())
 6: fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"), x = los,     densfun = "gamma")
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   2.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   2.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rpivotTableIntroduction.Rmd’

SUMMARY: processing the following file failed:
  ‘rpivotTableIntroduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rpolyhedra.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 49-88 (Rpolyhedra.Rmd) 
Error: processing vignette 'Rpolyhedra.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘Rpolyhedra.Rmd’

SUMMARY: processing the following file failed:
  ‘Rpolyhedra.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpredictit-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rpredictit-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘rpredictit-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following executable file:
  data/GH.RData
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.9Mb
Running ‘testthat.R’ [31m/38m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rsparse)
  > library(data.table)
  > library(Matrix)
  > options(rsparse_omp_threads = 1L)
  > logger = lgr::get_logger('rsparse')
  > logger$set_threshold('warn')
  > data("movielens100k")
  > test_check("rsparse")
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    4.9Mb
    libs  10.8Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    lib         1.4Mb
    libs        8.8Mb
    unitTests   1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rsyncrosim_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 15-19 (rsyncrosim_tutorial.Rmd) 
Error: processing vignette 'rsyncrosim_tutorial.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘rsyncrosim_tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘rsyncrosim_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R           1.4Mb
    bootstrap   1.8Mb
    data        2.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    rmarkdown   4.9Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    7.9Mb
    libs   2.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    doc   1.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   5.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    include   2.2Mb
    libs      2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc           3.3Mb
    htmlwidgets   1.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   3.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sankeywheel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘sankeywheel.Rmd’

SUMMARY: processing the following file failed:
  ‘sankeywheel.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    bin  10.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.3Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'pogs'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    example   2.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    5.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    docs      1.9Mb
    extdata   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data            1.5Mb
    vignette_data   2.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R   7.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   1.0Mb
    help      2.5Mb
Package required but not available: ‘x13binary’

Package suggested but not available for checking: ‘seasonalview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
Package which this enhances but not available for checking: ‘rsvg’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    4.2Mb
    libs   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.3Mb
Package suggested but not available for checking: ‘monocle’
Running ‘testthat.R’ [116s/146s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Seurat)
  Attaching SeuratObject
  > 
  > test_check("Seurat")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (19)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_load_10X.R:34:1): (code run outside of `test_that()`) ───────────
  Error: HDF5-API Errors:
      error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  
  Backtrace:
      █
   1. └─Seurat::Load10X_Spatial(data.dir = "../testdata/visium") test_load_10X.R:34:0
   2.   └─Seurat::Read10X_h5(...)
   3.     ├─infile[[paste0(genome, "/", feature_slot)]][]
   4.     └─hdf5r:::`[.H5D`(...)
   5.       └─x$read(...)
   6.         └─self$read_low_level(...)
  
  [ FAIL 1 | WARN 9 | SKIP 19 | PASS 587 ]
  Error: Test failures
  Execution halted
Running examples in ‘sfarrow-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_sf_dataset
> ### Title: Read an Arrow multi-file dataset and create 'sf' object
> ### Aliases: read_sf_dataset
> 
> ### ** Examples
> 
> # read spatial object
> nc <- sf::st_read(system.file("shape/nc.shp", package="sf"), quiet = TRUE)
> 
> # create random grouping
> nc$group <- sample(1:3, nrow(nc), replace = TRUE)
> 
> # use dplyr to group the dataset. %>% also allowed
> nc_g <- dplyr::group_by(nc, group)
> 
> # write out to parquet datasets
> # partitioning determined by dplyr 'group_vars'
> write_sf_dataset(nc_g, path = file.path(tempdir(), "ds"))
Warning: This is an initial implementation of Parquet/Feather file support and
geo metadata. This is tracking version 0.1.0 of the metadata
(https://github.com/geopandas/geo-arrow-spec). This metadata
specification may change and does not yet make stability promises.  We
do not yet recommend using this in a production setting unless you are
able to rewrite your Parquet/Feather files.
Error in all_record_batches(dots) : 
  Cannot call all_record_batches(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries. 
Calls: write_sf_dataset -> <Anonymous> -> all_record_batches
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example_sfarrow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-54 (example_sfarrow.Rmd) 
Error: processing vignette 'example_sfarrow.Rmd' failed with diagnostics:
Cannot call io___MemoryMappedFile__Open(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries. 
--- failed re-building ‘example_sfarrow.Rmd’

SUMMARY: processing the following file failed:
  ‘example_sfarrow.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘v1_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘v1_intro.Rmd’

--- re-building ‘v3_analyzing_landing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Quitting from lines 61-70 (v3_analyzing_landing.Rmd) 
Error: processing vignette 'v3_analyzing_landing.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘v3_analyzing_landing.Rmd’

SUMMARY: processing the following file failed:
  ‘v3_analyzing_landing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc      2.5Mb
    sqlite   1.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sf1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 208-210 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf6.Rmd’

--- re-building ‘sf7.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf7.Rmd’

SUMMARY: processing the following file failed:
  ‘sf5.Rmd’

Error: Vignette re-building failed.
Execution halted
X connection to :5.0 broken (explicit kill or server shutdown).
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGPdata.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-28 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGPdata.Rmd’

SUMMARY: processing the following file failed:
  ‘SGPdata.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP.Rmd’

--- re-building ‘SGP_Data_Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Analysis.Rmd) 
Error: processing vignette 'SGP_Data_Analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Analysis.Rmd’

--- re-building ‘SGP_Data_Preparation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Preparation.Rmd) 
Error: processing vignette 'SGP_Data_Preparation.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘SGP.Rmd’ ‘SGP_Data_Analysis.Rmd’ ‘SGP_Data_Preparation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    www   9.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    www  16.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data             1.3Mb
    shiny-examples   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Gadgets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Gadgets.Rmd’

--- re-building ‘Single-Layout.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Single-Layout.Rmd’

--- re-building ‘Split-Layout.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Split-Layout.Rmd’

--- re-building ‘Tabs-Layout.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Tabs-Layout.Rmd’

--- re-building ‘shinyMobile.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-14 (shinyMobile.Rmd) 
Error: processing vignette 'shinyMobile.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘shinyMobile.Rmd’

--- re-building ‘shinyMobile_tools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘shinyMobile_tools.Rmd’

SUMMARY: processing the following file failed:
  ‘shinyMobile.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    shinyApp  22.5Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    www   9.9Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    help   2.8Mb
    www    9.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_sidrar.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   2.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simplevis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning: Removed 2 rows containing non-finite values (stat_density).
old-style crs object detected; please recreate object with a recent sf::st_crs()
`summarise()` has grouped output by 'species'. You can override using the `.groups` argument.
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
`summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'sex'. You can override using the `.groups` argument.
old-style crs object detected; please recreate object with a recent sf::st_crs()
Quitting from lines 305-307 (simplevis.Rmd) 
Error: processing vignette 'simplevis.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘simplevis.Rmd’

SUMMARY: processing the following file failed:
  ‘simplevis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simrec-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 155-198 (simrec-vignette.Rmd) 
Error: processing vignette 'simrec-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘simrec-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘simrec-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘skm-vignettes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

skm_mls: auto_create g w.r.t first letter of s_name.

skm_mls: optimizing on k <1> ...

skm_mls: optimizing on k <1> ... done.

skm_mls: optimizing on k <2> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <2> ... done.

skm_mls: optimizing on k <3> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <3> ... done.

skm_mls: optimizing on k <4> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <4> ... done.

skm_mls: optimizing on k <5> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <5> ... done.

skm_mls: optimizing on k <6> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <6> ... done.

skm_mls: optimizing on k <7> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: encounter better solution at jk <42> run based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <7> ... done.

skm_mls: optimizing on k <8> ...
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   1.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    extdata   1.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘crypto101.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'crypto101.rmd' failed with diagnostics:
The file crypto101.md is not encoded in UTF-8. These lines contain invalid UTF-8 characters: 67
--- failed re-building ‘crypto101.rmd’

--- re-building ‘intro.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.rmd’

SUMMARY: processing the following file failed:
  ‘crypto101.rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘built_in.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘built_in.Rmd’

--- re-building ‘cloning.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘cloning.Rmd’

--- re-building ‘novel_solutions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘novel_solutions.Rmd’

--- re-building ‘understanding_sortable_js.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 85-86 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘understanding_sortable_js.Rmd’

--- re-building ‘using_custom_css.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘using_custom_css.Rmd’

SUMMARY: processing the following file failed:
  ‘understanding_sortable_js.Rmd’

Error: Vignette re-building failed.
Execution halted