Package suggested but not available for checking: ‘e1071’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Package required but not available: ‘dplyr’

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'Rglpk', 'qpmadr'

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

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

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

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

Package suggested but not available for checking: ‘ggplot2’

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'car', 'ggplot2', 'plyr', 'HH', 'Hmisc'

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'table1', 'googledrive', 'swfscMisc', 'geosphere', 'kableExtra',
  'gtsummary', 'ggplot2', 'gstat', 'sf', 'tmap', 'raster',
  'rnaturalearth'

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

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: ‘Rcpp’
Packages required but not available:
  'shiny', 'ggplot2', 'colourpicker', 'shinythemes', 'emojifont',
  'rintrojs'

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggplot2’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

VignetteBuilder package required for checking but not installed: ‘simplermarkdown’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘RSQLite’

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘testthat’

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'readr', 'stringr', 'hunspell'

Package suggested but not available for checking: ‘testthat’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exp2
> ### Title: Data from Experiment 2 in Gauvrit, Singmann, Soler-Toscano &
> ###   Zenil
> ### Aliases: exp2
> ### Keywords: dataset
> 
> ### ** Examples
> 
> 
> # load data
> data(exp2)
> 
> exp2$K <- acss(exp2$string, 6)[,"K.6"]
> 
> m_log <- glm(response ~ K, exp2, family = binomial)
> summary(m_log)

Call:
glm(formula = response ~ K, family = binomial, data = exp2)

Coefficients:
            Estimate Std. Error z value Pr(>|z|)    
(Intercept) -69.8169     9.9890  -6.989 2.76e-12 ***
K             1.9004     0.2709   7.015 2.30e-12 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 276.94  on 199  degrees of freedom
Residual deviance: 183.37  on 198  degrees of freedom
AIC: 187.37

Number of Fisher Scoring iterations: 5

> 
> # odds ratio of K:
> exp(coef(m_log)[2])
       K 
6.688694 
> 
> # calculate threshold of 0.5
> (threshold <- -coef(m_log)[1]/coef(m_log)[2])
(Intercept) 
   36.73763 
> 
> require(effects)
Loading required package: effects
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘effects’
> require(lattice)
Loading required package: lattice
> plot(Effect("K", m_log), rescale.axis = FALSE, ylim = c(0, 1))
Error in Effect("K", m_log) : could not find function "Effect"
Calls: plot
Execution halted
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Package required but not available: ‘GDINA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cosinor', 'cosinor2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'DiagrammeRsvg', 'ggplot2', 'readr', 'reshape2',
  'rmarkdown', 'scales', 'stringi', 'stringr', 'svglite'

Packages suggested but not available for checking:
  'gdistance', 'gWidgets2', 'gWidgets2tcltk', 'raster', 'sf', 'terra',
  'testthat'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dbplyr', 'dplyr', 'flextable', 'ggplot2', 'golem', 'lubridate',
  'modelr', 'patchwork', 'plyr', 'reactable', 'rmarkdown', 'RSQLite',
  'shiny', 'shinycssloaders', 'shinydashboard', 'shinydashboardPlus',
  'shinyFeedback', 'shinyjs', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'spelling', 'testthat', 'htmltools', 'officer', 'pkgload',
  'scales', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'geosphere', 'ggmap', 'lubridate', 'slider', 'xml2'

Packages suggested but not available for checking:
  'covr', 'lintr', 'ggplot2', 'mockery', 'rmarkdown', 'roxygen2',
  'styler', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Sigma0
> ### Title: \bar{sigma}_i computing using raw accelerometry data
> ### Aliases: Sigma0
> 
> ### ** Examples
> 
> filename = system.file("extdata","sample_GT3X+.csv.gz",package="ActivityIndex")
> res = ReadGT3XPlus(filename)
> hertz = res$Hertz
> x = res$Raw[ 1:1000, c("Time", "X", "Y", "Z")]
> res = Sigma0(x, hertz = hertz)
> testthat::expect_equal(res, c(SD = 0.184321637135534))
Error in loadNamespace(x) : there is no package called ‘testthat’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'ggplot2', 'tidyr', 'lubridate', 'devtools'

Package suggested but not available for checking: ‘testthat’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'stringi', 'xml2', 'openxlsx'

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘r2d3’

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', 'tidyr', 'dplyr', 'ConsRank'

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

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

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

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

Package suggested but not available for checking: ‘fda’

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

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

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

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: ‘extraDistr’

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

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

Packages suggested but not available for checking:
  'dqrng', 'parallelDist', 'rmarkdown', 'reshape2', 'ggplot2'

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

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/adaptivetau.Rcheck/00install.out’ for details.
Packages required but not available: 'Rcpp', 'rgl', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'glmnet', 'testthat', 'rmarkdown', 'dplyr'
checkRd: (-1) adapt.Rd:46: Lost braces
    46 | \item{qvals}{a vector of values in [0, 1]U{Inf}. Q-values. See Details}
       |                                           ^
checkRd: (-1) corr_lfdr.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_2d.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{plot_2d_lfdr} gives the contour plot of local FDR estimates when all p-values are equal to \code{targetp}. It is recommended to run \code{plot_2d_lfdr} for multiple \code{targetp}'s ranging from {0.001, 0.005, 0.01, 0.05}.
       |                                                                                                                                                                                                          ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'ggplot2', 'covr', 'rmarkdown', 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'spatstat', 'spatstat.geom', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'missForest', 'e1071', 'ComICS', 'pheatmap', 'pcaMethods', 'ranger'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
Packages required but not available: 'Rcpp', 'triebeard'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'miniUI', 'shiny', 'shinyjs', 'rmarkdown', 'rvest', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'miniUI', 'shinyFiles', 'stringr', 'dplyr', 'rmarkdown',
  'fs', 'DT'

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

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

Packages suggested but not available for checking:
  'covr', 'devtools', 'recipes', 'rmarkdown', 'roxygen2', 'spelling',
  'testthat', 'workflows'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in Rd file 'print.aTest.Rd':
  ‘how’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Package required but not available: ‘coneproj’

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

Packages suggested but not available for checking:
  'ade4TkGUI', 'adegraphics', 'adephylo', 'ape', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'adegraphics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rmarkdown', 'ROI.plugin.glpk', 'ROI.plugin.symphony'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ade4', 'igraph', 'ape', 'shiny', 'ggplot2', 'seqinr', 'reshape2',
  'dplyr'

Packages suggested but not available for checking:
  'adespatial', 'pegas', 'hierfstat', 'spdep', 'interp', 'poppr',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'latticeExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'adehabitatLT'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'adehabitatHR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) adeoptions.Rd:21-23: Lost braces
    21 |   \code{epsilon}{  the smallest significant distance between two points
       |                 ^
checkRd: (-1) adeoptions.Rd:25-27: Lost braces
    25 |   \code{shortprint}{  logical.  Defines whether special \code{show}
       |                    ^
Packages required but not available: 'ade4', 'phylobase', 'ape', 'adegenet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyBS', 'V8', 'shinyjs', 'shiny', 'dplyr', 'readr', 'tidyr',
  'haven', 'shinyWidgets'

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggplot2', 'lubridate', 'reshape2',
  'spelling', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ade4', 'adegraphics', 'adephylo', 'spdep', 'shiny'

Packages suggested but not available for checking:
  'ape', 'rmarkdown', 'betapart'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cubature', 'ggplot2', 'ggpubr', 'scales', 'latex2exp',
  'future.apply', 'progressr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'ggplot2', 'tidyr'
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'Rcpp', 'anytime', 'tidyr', 'dplyr', 'lubridate'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AdhereR', 'shiny', 'shinyWidgets', 'shinyjs', 'V8', 'colourpicker',
  'highlight', 'RMariaDB', 'RSQLite'

Packages suggested but not available for checking:
  'rmarkdown', 'readODS', 'readxl', 'haven', 'R.rsp'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ade4', 'adegraphics', 'ape', 'phylobase', 'phytools', 'rgl'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xml2', 'lubridate', 'dplyr', 'rvest'

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

Packages suggested but not available for checking:
  'Matching', 'WeightIt', 'eventglm', 'geepack', 'ggplot2', 'mice',
  'pammtools', 'pec', 'prodlim', 'riskRegression', 'rmarkdown',
  'testthat', 'tidyr', 'ggpp', 'vdiffr', 'covr'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adk_lake_shapes
> ### Title: Return path to Lake Polygons Shapefile
> ### Aliases: adk_lake_shapes
> 
> ### ** Examples
> 
> library(sf)
Error in library(sf) : there is no package called ‘sf’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) Amatdual.Rd:15: Lost braces
    15 |   \item{removelist}{a vector of indices into env{X} of the lifted coefficients during the transform (in the order of removal). }
       |                                                 ^
checkRd: (-1) fwtnp.Rd:30: Lost braces
    30 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'lubridate', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'lintr', 'pkgdown', 'testthat', 'miniUI', 'rmarkdown',
  'roxygen2', 'spelling', 'styler', 'usethis', 'covr', 'DT',
  'htmltools'

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

Packages suggested but not available for checking:
  'devtools', 'lintr', 'pkgdown', 'testthat', 'miniUI', 'rmarkdown',
  'roxygen2', 'spelling', 'stringr', 'usethis', 'covr', 'DT'

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

Packages suggested but not available for checking:
  'devtools', 'lintr', 'pkgdown', 'testthat', 'miniUI', 'rmarkdown',
  'roxygen2', 'spelling', 'usethis', 'covr', 'DT'

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

Packages suggested but not available for checking:
  'DT', 'htmltools', 'reactable', 'readxl', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'lintr', 'pkgdown', 'testthat', 'rmarkdown', 'roxygen2',
  'spelling', 'usethis', 'covr'
Packages required but not available:
  'admiral', 'admiraldev', 'dplyr', 'lubridate', 'metatools',
  'stringr', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'devtools', 'DT', 'lintr', 'miniUI', 'pkgdown', 'rmarkdown',
  'roxygen2', 'spelling', 'styler', 'testthat', 'usethis'

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

Packages suggested but not available for checking:
  'flexsurv', 'plyr', 'reshape2', 'testthat', 'rmarkdown', 'spelling'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ape', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘scales’

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'spatstat.geom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'learnr', 'BayesFactor', 'dplyr', 'car', 'effects', 'GGally',
  'ggplot2', 'Hmisc', 'readr', 'robust', 'sjstats', 'tidyr', 'WRS2'

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

Packages suggested but not available for checking: 'rmarkdown', '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: ‘R.rsp’

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fitaep.Rd:14: Lost braces
    14 | \item A sequence of goodness-of-fit measures consist of Akaike Information Criterion (\code{AIC}), Consistent Akaike Information Criterion (\code{CAIC}), Bayesian Information Criterion (\code{BIC}), Hannan-Quinn information criterion (\code{HQIC}), Anderson-Darling (\code{AD}), Cram\'{e}er-von Misses (\code{CVM}), Kolmogorov-Smirnov (\code{KS}), and log-likelihood (\code{log-likelihood}) statistics.
       |                                                                                                                                                                                                                                                                                              ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'ggvis', 'lubridate', 'plotly', 'ggplot2', 'tidyr', 'scales'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

Packages suggested but not available for checking:
  'dynlm', 'effects', 'forecast', 'mlogit', 'np', 'plm', 'rgl', 'ROCR',
  'rugarch', 'sampleSelection', 'systemfit', 'truncreg'

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

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'DescTools', 'kableExtra', 'rjags', 'ggmcmc',
  'spelling', 'testthat'

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

Packages suggested but not available for checking:
  'plyr', 'optimx', 'nloptr', 'rmarkdown', 'R.rsp', 'latticeExtra',
  'testthat', 'mlmRev', 'dplyr', 'tidyr', 'ggplot2', 'MEMSS',
  'effects', 'ggbeeswarm', 'cowplot', 'jtools', 'ggpubr', 'ggpol',
  'glmmTMB', 'brms', 'rstanarm', 'see', 'ez', 'ggResidpanel', 'vdiffr'

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'gstat', 'rgl', 'ggplot2', 'plyr', 'igraph', 'shiny',
  'shinyjs', 'scales', 'dbscan', 'mixtools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'drgee', 'stdReg', 'ivtools'

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

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', 'olsrr', 'ggplot2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'photobiology', 'R2jags', 'rstpm2'

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

Package suggested but not available for checking: ‘roxygen2’

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

Package suggested but not available for checking: ‘rmarkdown’

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

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: ‘rmarkdown’
Packages suggested but not available for checking: 'trustOptim', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running 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: ‘glmnet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/agop.Rcheck/00install.out’ for details.
Packages required but not available: 'plyr', 'spdep', 'spacetime', 'maxLik'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'lme4'
Running examples in ‘AgreementInterval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ai
> ### Title: ai
> ### Aliases: ai
> 
> ### ** Examples
> 
> ai(x=1:4, y=c(1, 1, 2, 4))
Error in loadNamespace(x) : there is no package called ‘lme4’
Calls: ai ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'miscF', 'lme4', 'R2jags'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'broom', 'car', 'desplot', 'dplyr', 'effects', 'equivalence',
  'FrF2', 'gge', 'ggplot2', 'gstat', 'HH', 'latticeExtra', 'lme4',
  'MCMCglmm', 'nullabor', 'pbkrtest', 'reshape2', 'rgdal', 'rmarkdown',
  'qicharts', 'qtl', 'SpATS', 'testthat'
checkRd: (-1) battese.survey.Rd:42: Lost braces
    42 |   emph{Journal of the American Statistical Association}, 83, 28-36.
       |       ^
checkRd: (-1) butron.maize.Rd:49: Lost braces
    49 |   Butron, A and Velasco, P and Ord{\'a}s, A and Malvar, RA (2004).
       |                                   ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lmerTest', 'pbkrtest', 'ggplot2'

Package suggested but not available for checking: ‘R.rsp’

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

Packages suggested but not available for checking:
  'DT', 'rmarkdown', 'roxygen2'

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'readxl', 'tidyr', 'ggplot2', 'igraph', 'formattable'

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'glmmTMB', 'lme4', 'maxlike', 'R2jags', 'jagsUI', 'lmerTest'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'edgeR', 'ALDEx2'

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

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

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

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

Package suggested but not available for checking: ‘onewaytests’

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

Packages suggested but not available for checking:
  'text2vec', 'tidytext', 'topicmodels', 'udpipe', 'quanteda',
  'quanteda.textmodels', 'rmarkdown', 'testthat'

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

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplyr’
Packages suggested but not available for checking:
  'rmarkdown', 'svglite', 'tinysnapshot'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'SuperLearner', 'ggplot2', 'future.apply', 'progressr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'dplyr', 'rvest', 'tidyr', 'stringr', 'xml2', 'readr',
  'readxl'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggplot2', 'ggseas', 'selectr', 'covr',
  'ggmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) CreateInputsPert.Rd:65: Lost braces
    65 | \emph{InputsPert}{[list] object of class \emph{InputsModel} containing the ensembles of perturbed model inputs required to perform data assimilation:}
       |                  ^
Packages required but not available: 'DiagrammeR', 'dplyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'caRamel', 'FME', 'ggmcmc', 'Rmalschains', 'GGally',
  'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dygraphs', 'shiny', 'shinyjs'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'lintr', 'testthat'
checkRd: (-1) get_airnow_area.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘stuve.pdf’
Packages required but not available:
  'mirt', 'tidyr', 'EstCRM', 'dplyr', 'ggplot2'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'dplyr', 'ggplot2', 'stringr', 'ggraph', 'tidygraph',
  'ggforce', 'textstem', 'tidytext', 'ggwordcloud', 'tidyfst'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.dke.fun.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item{las}{ Numeric in {0,1,2,3}; the style of axis labels. 
       |                          ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'shiny'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) interpp.Rd:119: Lost braces
   119 |   If \code{linear} is \\code{TRUE}, linear
       |                             ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'airr', 'ape', 'dplyr', 'igraph', 'Rcpp', 'readr',
  'scales', 'seqinr', 'stringi', 'tidyr', 'GenomicAlignments'

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

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking: 'eemR', 'EEM'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘optimx’

Packages suggested but not available for checking:
  'kableExtra', 'testthat', 'covr', 'rmarkdown', 'bookdown', 'ggplot2',
  'scales', 'reshape2'

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

Package suggested but not available for checking: ‘R.rsp’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'caret', 'seqinr', 'ROCR', 'reshape2', 'bio3d'

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', 'lubridate'

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

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

Packages suggested but not available for checking:
  'devtools', 'httptest', 'roxygen2', 'testthat', 'rmarkdown', 'covr',
  'spelling', 'fs'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
Package required but not available: ‘htmltools’

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'httptest2', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library (testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) amDataset.Rd:28: Lost braces
    28 | 		A code{matrix} or \code{data.frame} containing samples in rows and alleles in columns.\cr
       |                       ^
Package suggested but not available for checking: ‘pedigree’
Packages required but not available: 'BiodiversityR', 'adegenet'

Packages suggested but not available for checking:
  'poppr', 'dplyr', 'ggplot2', 'GGally', 'ggforce', 'ggrepel', 'ggsci',
  'gggibbous', 'gganimate', 'patchwork'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'htmlTable', 'plyr', 'readxl', 'reshape2', 'rio',
  'scales', 'stringr', 'survminer'

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'kableExtra', 'DT', 'googlesheets4'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping vignette re-building
Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’
Errors in running code in vignettes:
when running code in ‘intro.rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘intro.rmd’ using ‘UTF-8’... failed to complete the test
Packages suggested but not available for checking:
  'devtools', 'testthat', 'reshape2', 'rmarkdown', 'dplyr'
Running ‘testall.R’ [0s/0s]
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: 'lubridate', 'V8'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: episodes
> ### Title: Episodes
> ### Aliases: episodes
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'bife', 'car', 'rmarkdown'

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'interp', 'spatstat.geom', 'spatstat.random'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'pedigree', 'Rcpp', 'reshape', 'dplyr'

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'SuppDists', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'roxygen2'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'reticulate', 'htmlwidgets', 'vegawidget', 'repr'

Packages suggested but not available for checking:
  'readr', 'rmarkdown', 'listviewer', 'testthat', 'pryr', 'stringr',
  'tidyr', 'dplyr', 'pkgdown', 'V8', 'fs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fs', 'htmltools', 'rmarkdown', 'servr', 'tinkr', 'usethis', 'xml2'

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'kableExtra', 'readr', 'readxl',
  'rmarkdown', 'tidyr', 'tidyverse', 'webchem'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'sjmisc', 'xml2', 'furrr'

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

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

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

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

Packages suggested but not available for checking:
  'fields', 'ggplot2', 'RANN', 'rgl', 'RefManageR', 'rmarkdown', 'sf',
  'terra'

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

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

Packages suggested but not available for checking:
  'ggplot2', 'latex2exp', 'rmarkdown', 'testthat'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
'library' or 'require' call to ‘network’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
Packages required but not available: 'heatmaply', 'memoise', 'readxl'

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

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

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'latticeExtra', 'spam', 'bayesplot', 'Hmisc'

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

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

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

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

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

Packages suggested but not available for checking:
  'R.rsp', 'shiny', 'shinyBS', 'AICcmodavg'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'MplusAutomation', 'reshape2', 'stringr', 'plyr',
  'devtools', 'dplyr', 'stringi'

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

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

Packages suggested but not available for checking:
  'DT', 'ggplot2', 'pander', 'rmarkdown', 'shinythemes', 'spelling'

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

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'e1071'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'dplyr', 'readxl', 'rmarkdown', 'rvest', 'xml2'

Packages which this enhances but not available for checking:
  'ggplot2', 'janitor', 'skimr', 'tsibble'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’
Errors in running code in vignettes:
when running code in ‘welcome_to_AMR.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘welcome_to_AMR.Rmd’ using ‘UTF-8’... failed to complete the test
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ctmm', 'dplyr', 'FNN', 'lubridate', 'sf', 'sfheaders', 'terra',
  'tidyr'

Packages suggested but not available for checking:
  'adehabitatLT', 'broom', 'ggplot2', 'ggraph', 'geosphere', 'leaflet',
  'move', 'moveHMM', 'rmarkdown', 'suncalc', 'tidygraph'

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'aws.s3', 'arrow'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘princurve’

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', 'plotly', 'caret', 'htmltools', 'DT', 'RANN'

Package suggested but not available for checking: ‘rmarkdown’

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

Packages suggested but not available for checking:
  'testthat', 'tidyr', 'reshape2', 'rmarkdown', 'shiny'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Auto-generated content requiring editing in Rd file 'rowVars.Rd':
  \arguments: \dots: ‘~~Describe \code{\dots} here~~’
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Packages required but not available: 'glmnet', 'selectiveInference'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

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

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: 'rmarkdown', 'testthat'

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

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

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

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

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'shiny', 'htmltools', 'pryr', 'V8', 'servr'

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

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'servr', 'digest', 'RJSONIO', 'plyr', 'reshape2', 'scales'

Packages suggested but not available for checking:
  'gistr', 'shiny', 'htmltools', 'rmarkdown', 'testthat', 'devtools',
  'Hmisc', 'svglite', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'dplyr', 'keras', 'reticulate', 'tfdatasets', 'exifr',
  'av', 'imager'

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘shiny’

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

Package suggested but not available for checking: ‘TruncatedNormal’

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'DT', 'ggpubr', 'pheatmap', 'xml2'

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

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

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

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

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

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

Packages suggested but not available for checking:
  'testthat', 'stringr', 'bslib', 'sf', 'terra', 'keys',
  'colourpicker', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mc2d', 'EnvStats'

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

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

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

Packages suggested but not available for checking:
  'tidyverse', 'tidyquant', 'stringr', 'testthat', 'covr', 'rmarkdown',
  'devtools', 'roxygen2'

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

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

Package suggested but not available for checking: ‘lme4’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running 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:
  'gganimate', 'ggplot2', 'testthat', 'rmarkdown'
Running examples in ‘anscombiser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anscombise_gif
> ### Title: Animation of several Anscombised datasets
> ### Aliases: anscombise_gif
> 
> ### ** Examples
> 
> # Animate some Anscombe-like datasets produced using input1 to input8
> x <- list(input1, input2, input3, input4, input5, input6, input7, input8)
> idem <- c(FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE)
> anim <- anscombise_gif(x, idempotent = idem)
Error in anscombise_gif(x, idempotent = idem) : 
  Package ''ggplot2'' is required. Please install it.
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘caret’

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'antaresRead', 'antaresProcessing', 'spMaps', 'dygraphs', 'shiny',
  'plotly', 'htmltools', 'htmlwidgets', 'manipulateWidget', 'leaflet',
  'sf', 'lubridate', 'geojsonio', 'leaflet.minicharts', 'rAmCharts'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rhdf5', 'ggplot2', 'visNetwork', 'rmarkdown'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shapes', 'rgl', 'ddalpha', 'FNN', 'ICGE', 'biclust'

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

Package suggested but not available for checking: ‘testthat’

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

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

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

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'bookdown', 'rmarkdown', 'competitiontoolbox'
checkRd: (-1) PS-methods.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:65-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Sim-Functions.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:138-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:141-143: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'GGally', 'bayesplot', 'RcppArmadillo'

Packages suggested but not available for checking:
  'dendextend', 'ggdendro', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'xml2'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'readr', 'lubridate', 'vroom', 'stringr', 'usethis',
  'roxygen2'

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

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

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

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

Package suggested but not available for checking: ‘gettz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Running examples in ‘aod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iccbin
> ### Title: Intra-Cluster Correlation for Binomial Data
> ### Aliases: iccbin show,iccbin-method
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> data(rats)
> tmp <- rats[rats$group == "TREAT", ]
> # A: glmm (model linearization)
> iccbin(n, y, data = tmp, method = "A")
Error in loadNamespace(x) : there is no package called ‘lme4’
Calls: iccbin ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘lme4’
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                       ^
checkRd: (-1) gof.Rd:32: Lost braces
    32 | Assuming that the data length is \eqn{N} and the number of the parameters in the model is \eqn{p}, eqn{D} and eqn{X^2} are compared to a chi-squared distribution with \eqn{N-p} degrees of freedom.
       |                                                                                                                  ^
checkRd: (-1) iccbin.Rd:23: Lost braces
    23 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
checkRd: (-1) varbin.Rd:22: Lost braces
    22 |   \item{m}{A vector of the numbers of successes (proportions are eqn{y = m / n}).}
       |                                                                     ^
Running examples in ‘aods3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iccbin
> ### Title: Intra-Cluster Correlation for Clustered Binomial data
> ### Aliases: iccbin print.iccbin
> ### Keywords: datagen
> 
> ### ** Examples
> 
> data(rats)
> z <- rats[rats$group == "TREAT", ]
> # A: glmm (model linearization)
> iccbin(z$n, z$m, method = "A")
Error in loadNamespace(x) : there is no package called ‘lme4’
Calls: iccbin ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘roxygen2’

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

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

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'rmarkdown', 'scales', 'testthat',
  'units'

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

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

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

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

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'glmnet', 'rmarkdown', 'SurvMetrics', 'testthat',
  'units'

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

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available:
  'DT', 'shiny', 'shinydashboardPlus', 'shinydashboard', 'Rcpp',
  'RcppParallel', 'rstan', 'rstantools', 'dplyr', 'BayesFactor',
  'broom', 'car', 'highcharter', 'reshape', 'shinycssloaders',
  'stringr', 'waiter', 'htmltools', 'RcppEigen', 'StanHeaders'

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

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

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

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

Packages suggested but not available for checking:
  'cowplot', 'covr', 'rmarkdown', 'sf', 'spelling', 'testthat',
  'vdiffr'

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

Packages suggested but not available for checking: 'afex', 'ez', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘apaTables’

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

Packages suggested but not available for checking:
  'janitor', 'tidyr', 'covr', 'rmarkdown', 'kableExtra', 'testthat'

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'dplyr', 'igraph', 'reshape2', 'ggplot2', 'ggrepel', 'ggforce'

Packages suggested but not available for checking:
  'Spectrum', 'clusterProfiler', 'gprofiler2', 'DOSE', 'org.Hs.eg.db',
  'testthat', 'rmarkdown', 'stringr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Documented arguments not in \usage in Rd file 'apercu.Rd':
  ‘c’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'htmltools', 'htmlwidgets', 'ggplot2', 'shiny'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp', 'xml2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'rmarkdown', 'vdiffr'
checkRd: (-1) predict_adjust.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'episensr', 'shiny', 'golem', 'htmltools',
  'shinymaterial', 'shinyjs', 'rhandsontable', 'rmarkdown', 'ggraph',
  'igraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyBS', 'cowplot', 'dplyr', 'DT', 'ggplot2', 'htmltools',
  'plotly', 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vcdExtra', 'pROC'
Error(s) in re-building vignettes:
  ...
--- re-building ‘aplore3-examples.Rnw’ using knitr

Quitting from lines 5-6 [unnamed-chunk-15] (./ch/glow.Rnw)

Quitting from lines 5-6 (./ch/glow.Rnw)
Error: processing vignette 'aplore3-examples.Rnw' failed with diagnostics:
there is no package called 'vcdExtra'
--- failed re-building ‘aplore3-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘aplore3-examples.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'aplot', 'dplyr', 'ggfun', 'ggplot2', 'tidyr', 'ggstar',
  'yulab.utils'

Package suggested but not available for checking: ‘ggtree’

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

Package suggested but not available for checking: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) iconplot.Rd:172: Lost braces
   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
Packages required but not available:
  'dplyr', 'tidyr', 'flextable', 'officer'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'testthat', 'terra', 'dplyr', 'ggplot2',
  'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'ggplot2', 'tidyr'
Package required but not available: ‘rvest’

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

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

Packages suggested but not available for checking:
  'covr', 'isotree', 'modeldata', 'recipes', 'rmarkdown', 'spelling',
  'testthat', 'xml2'

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

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'DT', 'rhandsontable', 'shiny', 'shinythemes', 'sortable',
  'stringr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'ggplot2', 'tidyr'
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘testthat’

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

Packages suggested but not available for checking:
  'BayesianTools', 'chirps', 'daymetr', 'FedData', 'ggplot2',
  'listviewer', 'metrica', 'nasapower', 'nloptr', 'reactR',
  'rmarkdown', 'sensitivity', 'soilDB', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
Packages required but not available: 'erer', 'car'

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

Packages suggested but not available for checking:
  'testthat', 'survey', 'srvyr', 'vdiffr', 'covr', 'rmarkdown'

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

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

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'stringr', 'farver'

Packages suggested but not available for checking:
  'ape', 'soilDB', 'sf', 'latticeExtra', 'tactile', 'compositions',
  'sharpshootR', 'markovchain', 'testthat', 'Gmedian', 'Hmisc',
  'scales', 'digest', 'rmarkdown', 'plyr'

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

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
Packages required but not available:
  'ggplot2', 'qqplotr', 'Rcpp', 'RcppArmadillo'

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

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'hdrcde', 'shiny', 'readr', 'toOrdinal', 'ggplot2', 'ggalt',
  'reshape2', 'dplyr', 'digest', 'gplots', 'ggraph'

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

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

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

Packages suggested but not available for checking:
  'broom', 'caret', 'covr', 'gtsummary', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘geometry’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/archive.Rcheck/00install.out’ for details.
Packages required but not available:
  'anytime', 'dplyr', 'ggplot2', 'lubridate', 'rvest', 'stringr',
  'tidyr', 'xml2'

Packages suggested but not available for checking:
  'vcr', 'testthat', 'webmockr'

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

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

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: post_process_pbf
> ### Title: Post process pbf results
> ### Aliases: post_process_pbf
> 
> ### ** Examples
> 
> tbl_fp <- system.file("small-table.pbf", package = "arcpbf")
> fc_fp <- system.file("small-points.pbf", package = "arcpbf")
> 
> # table feature collection
> fc <- read_pbf(tbl_fp)
> head(post_process_pbf(fc))
  OBJECTID       Adoption_Service_Provider  DBA       city                state
1        1 A Family in Bloom Adoption, LLC <NA>    Boulder             Colorado
2        2     A Love Beyond Borders, Inc. <NA>     Denver             Colorado
3        3                  Adopolis, Inc. <NA> Washington District of Columbia
   Accreditation_or_Approval_Statu Accredited_Approvedto_Provide
1 Accredited/Approved – In Process         Incoming and Outgoing
2                         Approved                      Incoming
3                       Accredited                      Incoming
                                          full_address
1           Adoption Service Provider,Boulder,Colorado
2      A Family in Bloom Adoption, LLC,Denver,Colorado
3 A Love Beyond Borders, Inc.,Washington,Washington DC
> 
> # feature collection with geometry
> fc <- read_pbf(fc_fp)
Error in post_process_single(x, use_sf) : 
  The package "sf" is required to create `sf` objects.
Calls: read_pbf ... post_process_pbf -> post_process_single -> <Anonymous>
Execution halted
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Packages required but not available:
  'sf', 'dplyr', 'ggplot2', 'tidyr', 'raster', 'DT'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'rvest', 'xml2', 'stringr', 'cowplot',
  'magick'

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

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

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

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

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

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_ards
> ### Title: Adds data to an Analysis Results Dataset
> ### Aliases: add_ards
> 
> ### ** Examples
> 
> library(ards)
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'readr', 'sf', 'stringr', 'tidyr', 'tabshiftr',
  'ontologics', 'rmapshaper'

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

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:
  'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/area.Rcheck/00install.out’ for details.
Packages required but not available:
  'tidyr', 'dplyr', 'shiny', 'shinydashboard', 'shinyBS', 'shinyjs',
  'ggplot2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ingredients', 'iBreakDown', 'gistr', 'plumber', 'auditor', 'DALEX',
  'fairmodels'

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

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

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

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

Packages suggested but not available for checking:
  'colourpicker', 'lubridate', 'rmarkdown', 'shiny', 's2', 'sf',
  'testthat', 'shinyBS'

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

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘run-all.R’ [0s/0s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'hommel', 'RNifti', 'plyr'

Package suggested but not available for checking: ‘rmarkdown’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DescribeDF', 'dplyr', 'forecast', 'e1071'

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'text2speech', 'rmarkdown', 'xml2', 'rvest'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'readr', 'spelling', 'dplyr', 'dbplyr', 'testthat', 'covr',
  'fs', 'rmarkdown', 'RSQLite', 'duckdb', 'vroom', 'future.apply'
Running examples in ‘arkdb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arkdb_delete_db
> ### Title: delete the local arkdb database
> ### Aliases: arkdb_delete_db
> 
> ### ** Examples
> 
> 
> # Create a db
> dir <- tempfile()
> db <- local_db(dir)
Error in db_driver(dbname, driver = driver, read_only = read_only) : 
  No drivers found. see ?arkdb::local_db
Calls: local_db -> db_driver
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'qvalue', 'ComplexHeatmap'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.AR1
> ### Title: Precision matrix for an AR1 process
> ### Aliases: Q.AR1 r.AR1
> 
> ### ** 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’
> # simulate AR1 GMRF
> obs <- r.AR1(100, M=30, sigma=1, rho=.98)
> # resulting matrix is n x M
> dim(obs)
[1] 100  30
> # subtract off the first time point to more easily observe correlation
> obs_adj <- obs - obs[,1]
> # move objects to a data frame
> ar1_df <- data.frame(obs=c(t(obs_adj)), realization=rep(1:100, each=30),
+                      time=rep(1:30, 100))
> # plot each realization
> ggplot(data=ar1_df, aes(time, obs, group=realization, color=realization)) +
+     geom_line()
Error in ggplot(data = ar1_df, aes(time, obs, group = realization, color = realization)) : 
  could not find function "ggplot"
Execution halted
Package required but not available: ‘lme4’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'np', 'Hmisc', 'spatstat.geom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'aroma.core', 'R.cache', 'R.filesets', 'future'

Packages suggested but not available for checking:
  'affxparser', 'oligo', 'oligoClasses', 'pdInfoBuilder'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'aroma.core', 'R.filesets', 'R.cache', 'PSCBS', 'future.apply'

Package suggested but not available for checking: ‘GLAD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'R.filesets', 'R.cache', 'R.rsp', 'PSCBS', 'future'

Packages suggested but not available for checking:
  'EBImage', 'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'alphashape3d', 'compositions', 'geometry', 'Morpho', 'rgl', 'Rvcg',
  'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'readr', 'stringr', 'tm', 'tidyr', 'eurostat',
  'sf', 'ggplot2', 'archive', 'future', 'future.apply'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'plyr', 'reshape2', 'dplyr', 'ggplot2', 'viridis',
  'rmarkdown', 'testthat'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running 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: ‘gmp’

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'dbplyr', 'decor', 'dplyr', 'duckdb', 'lubridate', 'pkgload',
  'reticulate', 'rmarkdown', 'stringi', 'stringr', 'testthat', 'tzdb'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/arrow.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'broom', 'rmarkdown', 'testthat', 'pander', 'pROC', 'geepack'
Running examples in ‘arsenal-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: modelsum
> ### Title: Fit models over each of a set of independent variables with a
> ###   response variable
> ### Aliases: modelsum
> 
> ### ** Examples
> 
> 
> data(mockstudy)
> 
> tab1 <- modelsum(bmi ~ sex + age, data = mockstudy)
Error in check_pkg("broom") : 
  Package 'broom' is required for this functionality, but is not installed.
Calls: modelsum -> modelsum_guts -> check_pkg
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ars.Rcheck/00install.out’ for details.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'dplyr'
Running examples in ‘arthistory-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: artists
> ### Title: Artists by edition of Gardner or Janson's art history textbook
> ### Aliases: artists
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘shiny’

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

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

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2', 'tidyr', 'pander', 'lmerTest',
  'phia', 'stringi', 'DescTools', 'covr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ambient', 'e1071', 'ggplot2', 'kknn', 'Rcpp', 'scales',
  'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'pmml', 'arulesViz', 'arulesCBA', 'testthat'
Running examples in ‘arules-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pmml
> ### Title: Read and Write PMML
> ### Aliases: pmml write.PMML read.PMML
> ### Keywords: interface
> 
> ### ** Examples
> 
> data("Groceries")
> 
> rules <- apriori(Groceries, parameter = list(support = 0.001))
Apriori

Parameter specification:
 confidence minval smax arem  aval originalSupport maxtime support minlen
        0.8    0.1    1 none FALSE            TRUE       5   0.001      1
 maxlen target  ext
     10  rules TRUE

Algorithmic control:
 filter tree heap memopt load sort verbose
    0.1 TRUE TRUE  FALSE TRUE    2    TRUE

Absolute minimum support count: 9 

set item appearances ...[0 item(s)] done [0.00s].
set transactions ...[169 item(s), 9835 transaction(s)] done [0.01s].
sorting and recoding items ... [157 item(s)] done [0.00s].
creating transaction tree ... done [0.00s].
checking subsets of size 1 2 3 4 5 6 done [0.02s].
writing ... [410 rule(s)] done [0.00s].
creating S4 object  ... done [0.00s].
> rules <- head(rules, by = "lift")
> rules
set of 6 rules 
> 
> ### save rules as PMML
> write.PMML(rules, file = "rules.xml")
Error in as.vector(x, "character") : 
  cannot coerce type 'closure' to vector of type 'character'
Calls: write.PMML -> check_installed
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/arulesSequences.Rcheck/00install.out’ for details.
Packages required but not available:
  'igraph', 'ggplot2', 'ggraph', 'tidyr', 'dplyr', 'DT', 'plotly',
  'visNetwork'

Packages suggested but not available for checking:
  'tidygraph', 'shiny', 'shinythemes', 'htmlwidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'rmarkdown', 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'gWidgets2', 'gWidgets2tcltk'

Package suggested but not available for checking: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'magick', 'V8'

Packages suggested but not available for checking:
  'covr', 'decor', 'htmlwidgets', 'mockery', 'rmarkdown', 'testthat'

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

Package suggested but not available for checking: ‘Hmisc’

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'spdep'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'alphahull', 'alphashape3d', 'Rvcg', 'TDA', 'dplyr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'exact2x2', 'exactci', 'bpcp'

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

Packages suggested but not available for checking:
  'covr', 'miniUI', 'rmarkdown', 'shiny', 'shinycssloaders',
  'spelling', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘digest’

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

Package suggested but not available for checking: ‘rmarkdown’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_network
> ### Title: Calculating Weighted Network
> ### Aliases: get_network
> 
> ### ** Examples
> 
> data("group_by_individual")
> data("times")
> 
> # subset GBI (to reduce run time of the example)
> gbi <- gbi[,1:80]
> 
> ## define to 2 x N x N network to hold two association matrices
> networks <- array(0, c(2, ncol(gbi), ncol(gbi)))
> 
> ## calculate network for first half of the time
> networks[1,,] <- get_network(gbi, data_format="GBI",
+ 	association_index="SRI", times=times, start_time=0, 
+ 	end_time=max(times)/2)
Generating  80  x  80  matrix
> networks[2,,] <- get_network(gbi, data_format="GBI",
+ 	association_index="SRI", times=times, 
+ 	start_time=max(times)/2, end_time=max(times))
Generating  80  x  80  matrix
> 
> ## test if one predicts the other via a mantel test (must be loaded externally)
> library(ape)
Error in library(ape) : there is no package called ‘ape’
Execution halted
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sem’
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'dplyr', 'tidyr', 'splines2', 'Rcpp'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'V8', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'shiny', 'testthat'
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                    ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                 ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                          ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Unknown packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘dplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
Running ‘testthat.R’ [0s/1s]
Running 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:
  'rmarkdown', 'AER', 'faraway', 'testthat'
Running examples in ‘assessor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: resid_semiconti
> ### Title: Residuals for regression models with semicontinuous outcomes
> ### Aliases: resid_semiconti
> 
> ### ** Examples
> 
> ## Tweedie model
> library(tweedie)
> library(statmod)
> n <- 500
> x11 <- rnorm(n)
> x12 <- rnorm(n)
> beta0 <- 5
> beta1 <- 1
> beta2 <- 1
> lambda1 <- exp(beta0 + beta1 * x11 + beta2 * x12)
> y1 <- rtweedie(n, mu = lambda1, xi = 1.6, phi = 10)
> # Choose parameter p
> # True model
> model1 <-
+   glm(y1 ~ x11 + x12,
+     family = tweedie(var.power = 1.6, link.power = 0)
+   )
> resid.tweedie <- resid_semiconti(model1)
> 
> ## Tobit regression model
> library(VGAM)
Loading required package: stats4
Loading required package: splines
> beta13 <- 1
> beta14 <- -3
> beta15 <- 3
> 
> set.seed(1234)
> x11 <- runif(n)
> x12 <- runif(n)
> lambda1 <- beta13 + beta14 * x11 + beta15 * x12
> sd0 <- 0.3
> yun <- rnorm(n, mean = lambda1, sd = sd0)
> y <- ifelse(yun >= 0, yun, 0)
> 
> # Using VGAM package
> # True model
> fit1 <- vglm(formula = y ~ x11 + x12, tobit(Upper = Inf, Lower = 0, lmu = "identitylink"))
> # Missing covariate
> fit1miss <- vglm(formula = y ~ x11, tobit(Upper = Inf, Lower = 0, lmu = "identitylink"))
> 
> resid.tobit1 <- resid_semiconti(fit1, plot = TRUE)
> resid.tobit2 <- resid_semiconti(fit1miss, plot = TRUE)
> 
> # Using AER package
> library(AER)
Error in library(AER) : there is no package called ‘AER’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'RiskPortfolios', 'riskParityPortfolio'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'caret', 'e1071', 'ggplot2', 'reshape2', 'stringr'

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

Packages suggested but not available for checking:
  'asteRiskData', 'BiocStyle', 'plotly', 'dplyr', 'ggmap', 'rmarkdown'

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute.ALD
> ### Title: Compute ALD.
> ### Aliases: compute.ALD
> 
> ### ** Examples
> 
> library(asymLD)
> 
> # An example using haplotype frequencies from Wilson(2010)
> data(hla.freqs)
> hla.a_b <- hla.freqs[hla.freqs$locus1=="A" & hla.freqs$locus2=="B",]
> compute.ALD(hla.a_b)
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2       F.1    F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      A      B 0.1021811 0.340332 0.04876543 0.1903394 0.5150291 0.3857872
> hla.freqs$locus <- paste(hla.freqs$locus1, hla.freqs$locus2, sep="-")
> compute.ALD(hla.freqs[hla.freqs$locus=="C-B",])
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2        F.1     F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      C      B 0.08637241 0.7350216 0.05040254 0.4520268 0.8425979 0.6503396
> # Note: additonal columns on the input dataframe (e.g., "locus" above) are allowed, but
> # ignored by the function.
> 
> # An example using genotype data from the haplo.stats package
> require(haplo.stats)
Loading required package: haplo.stats
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘haplo.stats’
> data(hla.demo)
Warning in data(hla.demo) : data set ‘hla.demo’ not found
> geno <- hla.demo[,5:8]  #DPB-DPA
Error: object 'hla.demo' not found
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'gplots', 'smacof'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'rmarkdown', 'spelling', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'later', 'promises', 'testthat', 'stringr'

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

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

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

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

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

Package suggested but not available for checking: ‘rtop’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggplot2'
checkRd: (-1) simulation_dgp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
checkRd: (-1) simulation_dgp.Rd:23: Lost braces
    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'stringi', 're2', 'binsegRcpp', 'fpop',
  'LOPART', 'PeakSegDisk', 'readr', 'dplyr', 'tidyr'
Packages required but not available: 'leaflet', 'shiny'

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

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

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

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

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', 'stringr', 'terra'

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

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

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

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'ggraph', 'igraph', 'magick', 'rmarkdown',
  'testthat', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unknown package ‘snpar’ in Rd xrefs
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rmarkdown', 'roxygen2', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'covr', 'spelling'
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'lubridate', 'lme4', 'arm', 'stringr', 'ggplot2'

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

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

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

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

Packages suggested but not available for checking:
  'rmarkdown', 'ggbeeswarm', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) audioSample.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) audioSample.Rd:21: Lost braces in \itemize; meant \describe ?
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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:
  'DALEX', 'ggplot2', 'ggrepel', 'scales'

Packages suggested but not available for checking:
  'r2d3', 'rmarkdown', 'spelling', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rBayesianOptimization', 'xgboost', 'ggplot2', 'readr', 'stringr',
  'lubridate', 'narray', 'imputeTS', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'memoise', 'readr', 'stringi', 'V8'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using knitr

Quitting from lines 72-79 [JoinData] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘my-vignette.Rmd’

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

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

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

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

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

Packages suggested but not available for checking:
  'testthat', 'kernlab', 'ggplot2', 'penaltyLearning', 'covr',
  'ggrepel'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plyr', 'betapart', 'r2r', 'stringr'

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

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:
  'rmarkdown', 'spelling', 'testthat'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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:
  'xgboost', 'e1071', 'caret', 'CORElearn', 'infotheo', 'minerva'

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', 'Rcpp', 'RcppParallel', 'RcppArmadillo'

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'spam', 'fields', 'filehashSQLite', 'filehash', 'LatticeKrig', 'FNN',
  'Rcpp', 'RSpectra', 'RcppEigen', 'RcppParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'dplyr', 'enrichR', 'ape', 'ComplexHeatmap', 'DESeq2',
  'ggplot2', 'ggrepel', 'GSVA', 'openxlsx', 'reshape2', 'stringr',
  'textshape', 'tidyr'

Package suggested but not available for checking: ‘rmarkdown’

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

Packages suggested but not available for checking:
  'readxl', 'xml2', 'rvest', 'testthat'

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'spatstat.geom', 'gear', 'broom', 'rmarkdown'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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:
  'gstat', 'reshape', 'ggplot2', 'sf', 'stars'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'lme4', 'gbm', 'e1071', 'glmmLasso', 'EBMAforecast',
  'doRNG', 'ggplot2', 'tidyr', 'vglmer', 'stringr'

Package suggested but not available for checking: ‘R.rsp’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'annotate', 'fgsea', 'org.Hs.eg.db', 'Rtsne', 'clusterProfiler',
  'msigdbr'

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'e1071', 'echarts4r', 'lubridate', 'quanteda',
  'quanteda.textstats', 'scales'

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'moonBook', 'dplyr', 'stringr', 'tidyr', 'mice', 'officer',
  'flextable', 'patchwork', 'ggplot2', 'broom', 'tidycmprsk', 'scales',
  'pammtools'

Packages suggested but not available for checking:
  'finalfit', 'lme4', 'rmarkdown', 'survminer', 'PairedData'

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tableone', 'pROC', 'ggplot2', 'Hmisc', 'car', 'coxed', 'dplyr',
  'tidyr', 'plotly', 'randomForestSRC', 'survAUC', 'survminer'

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘roxygen2’

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

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

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

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

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'rmarkdown', 'spelling', 'styler',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘matlab2r’

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

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

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'selectiveInference', 'VariableScreening', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xml2', 'dplyr', 'readr', '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:
  'readxl', 'ggplot2', 'stringr', 'tidyr', 'ggthemes', 'reshape2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'rmarkdown', 'e1071'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'janitor', 'rmarkdown', 'lubridate', 'tidyr',
  'ggrepel'
Packages suggested but not available for checking: 'testthat', 'ggplot2'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/av.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'rmarkdown', 'covr', 'spelling'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'kohonen', 'shiny', 'htmlwidgets', 'bslib', 'rmarkdown', 'htmltools',
  'rclipboard', 'ggplot2', 'viridis', 'DT', 'kernlab', 'fields',
  'e1071', 'haven', 'readxl', 'readODS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'ggplot2', 'tidyr'
Packages required but not available: 'aws.signature', 'xml2', 'dplyr'

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rjson', 'aws.signature', 'xml2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xml2', 'aws.signature'

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

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

Packages suggested but not available for checking:
  'testthat', 'aws.s3', 'aws.iam'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'xml2', 'digest', 'aws.signature'

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'httpuv', 'shiny', 'shinyjs'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'plumber', 'RestRserve'
Running ‘testthat.R’ [0s/1s]
Running 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:
  'AzureTableStor', 'odbc', 'dplyr', 'testthat', 'rmarkdown'
checkRd: (-1) cosmos_mongo.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
Running ‘testthat.R’ [0s/1s]
Running 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: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'AzureStor', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reticulate', 'plyr', 'DT', 'htmltools', 'servr', 'shiny',
  'shinycssloaders'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'httpuv', 'AzureStor'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘xml2’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nlmixr2', 'digest', 'nlmixr2est', 'nonmem2rx', 'qs', 'rxode2',
  'Rcpp', 'RcppArmadillo', 'RcppEigen', 'rxode2parse'

Packages suggested but not available for checking:
  'testthat', 'lixoftConnectors', 'PKNCA', 'rmarkdown', 'spelling',
  'units'

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

Package suggested but not available for checking: ‘R.rsp’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SPOT', 'dplyr', 'ggplot2', 'golem', 'igraph', 'lubridate',
  'markovchain', 'padr', 'rvest', 'scales', 'simmer', 'slider',
  'testthat', 'plyr', 'xml2'

Packages suggested but not available for checking:
  'batchtools', 'rmarkdown', 'simmer.plot', 'stringr', 'tidyverse',
  'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'dplyr', 'rmarkdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘calibrator’

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

Packages suggested but not available for checking:
  'pander', 'fields', 'testthat', 'pcalg', 'rmarkdown'

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'parsnip', 'butcher', 'C50', 'dials', 'dplyr', 'furrr', 'rsample',
  'tidyr'

Packages suggested but not available for checking:
  'AmesHousing', 'covr', 'modeldata', 'recipes', 'rmarkdown',
  'spelling', 'testthat', 'yardstick'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'scales'
Packages required but not available:
  'rjags', 'R2jags', 'lubridate', 'robCompositions', 'ggplot2',
  'ggpubr', 'reshape2', 'shinyFiles', 'shinydashboard'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'rmarkdown', 'covr', 'knitcitations', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'dplyr', 'tidyr',
  'Hmisc', 'ggplot2', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'rmarkdown', 'DESeq2', 'pheatmap', 'Ckmeans.1d.dp'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'stringr',
  'tidyr', 'multidplyr', 'ggplot2', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'scales', 'networkD3', 'testthat', 'fields', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppDist'

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘future’

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

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:
  'rjags', 'R2jags', 'ggplot2', 'ggExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'distributions3', 'MBA'

Packages suggested but not available for checking:
  'ff', 'fields', 'interp', 'rjags', 'BayesX', 'sf', 'spatstat',
  'spdep', 'keras', 'splines2', 'sdPrior', 'glmnet', 'scoringRules',
  'rmarkdown', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'RSpectra', 'dplyr', 'igraph', 'leaflet', 'animation',
  'future', 'furrr', 'Rcpp', 'RcppArmadillo'

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

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

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

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bamp.Rcheck/00install.out’ for details.
Package required but not available: ‘mice’

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'rfPermute', '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: 'rvest', 'stringr', 'xml2'

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

Package suggested but not available for checking: ‘ArrayExpress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Packages required but not available: 'DT', 'miniUI', 'shiny'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BART', 'e1071', 'rmarkdown', 'roxygen2', 'testthat', 'covr'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bark.Rcheck/00install.out’ for details.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'mvnfast', 'RcppArmadillo'

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

Packages suggested but not available for checking:
  'testthat', 'lme4', 'tmle', 'stan4bart'

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

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

Packages suggested but not available for checking:
  'furrr', 'future', 'ggrepel', 'progressr', 'qs', 'reshape2',
  'rmarkdown', 'RSQLite', 'scales', 'stringi', 'testthat', 'usethis',
  'xml2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘coneproj’
Packages suggested but not available for checking:
  'gWidgets2', 'gWidgets2tcltk'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'slippymath', 'terra', 'magick'

Packages suggested but not available for checking:
  'rgdal', 'ggplot2', 'mapview', 'mapedit', 'raster', 'stars',
  'testthat', 'covr'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dummyClassifier
> ### Title: a method used for the train function in caret
> ### Aliases: dummyClassifier
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # Split the data into training and testing sets
> set.seed(2023)
> index <- sample(1:nrow(iris), nrow(iris) * 0.8)
> train_data <- iris[index,]
> test_data <- iris[-index,]
> 
> ctrl1 <- caret::trainControl(method = "none")
Error in loadNamespace(x) : there is no package called ‘caret’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'rms', 'do'

Package suggested but not available for checking: ‘rmarkdown’

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

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'GO.db', 'GSEABase', 'org.Hs.eg.db',
  'reactome.db', 'rmarkdown', 'spelling', 'testthat'

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

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

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

Packages suggested but not available for checking:
  'lubridate', 'listviewer', 'openxlsx', 'flextable', 'officer',
  'shiny', 'rmarkdown', 'testthat'

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plyr', 'dplyr', 'tidyr', 'ggrepel', 'scales',
  'ggplotify', 'dendextend', 'PBSmapping', 'stringr', 'GGally',
  'ggnetwork', 'readr'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'GGally', 'rmarkdown', 'roxygen2', 'dplyr', 'glmbb',
  'testthat', 'covr', 'faraway'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping vignette re-building
Packages suggested but not available for checking: 'R.rsp', 'testthat'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fs', 'lubridate'

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

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

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

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

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

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'tidyr', 'ggplot2', 'RcppArmadillo', 'testthat'

Packages suggested but not available for checking: 'xml2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'broom', 'dplyr', 'geepack', 'ggplot2', 'stringr', 'tidyr'

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

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

Packages suggested but not available for checking:
  'e1071', 'future', 'future.batchtools', 'ranger', 'rmarkdown',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'concaveman', 'dplyr', 'latex2exp', 'vtable'

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘testthat’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Anthropometry', 'plyr', 'dplyr', 'ggplot2', 'lubridate',
  'qdapRegex', 'readr', 'reshape2', 'rvest', 'rworldmap', 'scales',
  'stringi', 'stringr', 'tidyr', 'xml2'

Package suggested but not available for checking: ‘rmarkdown’

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

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

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

Package suggested but not available for checking: ‘testthat’

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

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:
  'Rcpp', 'MCMCpack', 'SuppDists', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'cowplot', 'dplyr', 'ggplot2', 'reshape', 'rstan',
  'rstantools', 'mcmcse', 'RcppParallel', 'StanHeaders', 'RcppEigen'

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

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) coupledMetropolis.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:86-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:92-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:95-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:98-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:110-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:113-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:116-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:119-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:122-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:125-127: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'ggplot2', 'RISmed', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'rmarkdown', 'shiny', 'highcharter', 'DT', 'shinydashboard',
  'dashboardthemes', 'shinyalert', 'shinyjs', 'openxlsx', 'tidyverse'

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

Package suggested but not available for checking: ‘R.rsp’

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MCMCpack’
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) bayesDccGarch.Rd:91: Lost braces; missing escapes or markup?
    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
checkRd: (-1) bayesDccGarch.Rd:92: Lost braces; missing escapes or markup?
    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'ggplot2', 'Rcpp', 'reshape2', 'rstantools', 'rstan',
  'RcppEigen', 'RcppParallel', 'StanHeaders'

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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:
  'readxl', 'testthat', 'rmarkdown', 'ggfortify', 'condSURV'

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

Package suggested but not available for checking: ‘testthat’

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

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

Packages suggested but not available for checking:
  'covr', 'dplyr', 'geometry', 'ggplot2', 'INLA', 'rdist', 'rmarkdown',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'ggplot2', 'forecast', 'Rcpp', 'rstan', 'rstantools',
  'RcppParallel', 'bridgesampling', 'StanHeaders', 'lubridate',
  'prophet', 'RcppEigen'

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) gMLE.bb.Rd:18: Lost braces
    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
Skipping checking math rendering: package 'V8' unavailable
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BayesGPfit.Rcheck/00install.out’ for details.
Packages required but not available:
  'AquaticLifeHistory', 'bayesplot', 'dplyr', 'ggplot2', 'Rcpp',
  'RcppParallel', 'rstan', 'rstantools', 'tidybayes', 'RcppEigen',
  'StanHeaders'

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bayesianETAS.Rcheck/00install.out’ for details.
Packages required but not available:
  'MCMCpack', 'reshape2', 'ggplot2', 'nse'

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

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:
  'DoseFinding', 'ggplot2', 'nloptr', 'RBesT'

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

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'heatmaply', 'networkD3', 'plotly', 'rintrojs', 'shiny', 'shinyAce',
  'shinydashboard', 'shinyWidgets'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'ggplot2', 'ggpubr', 'laGP', 'lhs', 'Rcpp', 'RcppParallel',
  'reshape', 'rstantools', 'stringr', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘rmarkdown’

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

Packages suggested but not available for checking:
  'covr', 'devtools', 'future', 'recipes', 'rmarkdown', 'roxygen2',
  'rstan', 'spelling', 'testthat', 'workflows'

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

Packages suggested but not available for checking:
  'patchwork', 'rmarkdown', 'testthat', 'vdiffr', 'webshot2'

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

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

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

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

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

Packages suggested but not available for checking:
  'mcmcse', 'PottsUtils', 'rstan', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'e1071', 'fields', 'MCMCpack'

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

Package suggested but not available for checking: ‘wpp2015’

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

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BayesLogit.Rcheck/00install.out’ for details.
Packages required but not available:
  'Rcpp', 'ggplot2', 'igraph', 'RcppArmadillo', 'testthat'

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

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mainEff
> ### Title: Main Effects
> ### Aliases: mainEff
> 
> ### ** Examples
> 
> 
> ## Importing Data, generating BMB object
> y <- importObservations(file = system.file("extdata", "twonode_example.csv",
+                                     package = "BayesMassBal"),
+                    header = TRUE, csv.params = list(sep = ";"))
> 
> C <- matrix(c(1,-1,0,-1,0,0,1,-1,0,-1), byrow = TRUE, ncol = 5, nrow = 2)
> X <- constrainProcess(C = C)
> 
> BMB_example <- BMB(X = X, y = y, cov.structure = "indep",
+                    BTE = c(10,200,1), lml = FALSE, verb=0)
> 
> fn_example <- function(X,ybal){
+     cu.frac <- 63.546/183.5
+     feed.mass <- ybal$CuFeS2[1] + ybal$gangue[1]
+     ## Concentrate mass per ton feed
+     con.mass <- (ybal$CuFeS2[3] + ybal$gangue[3])/feed.mass
+     ## Copper mass per ton feed
+     cu.mass <- (ybal$CuFeS2[3]*cu.frac)/feed.mass
+     gam <- c(-1,-1/feed.mass,cu.mass,-con.mass,-cu.mass,-con.mass)
+     f <- X %*% gam
+     return(f)
+     }
> 
> rangex <- matrix(c(4.00 ,6.25,1125,1875,3880,9080,20,60,96,208,20.0,62.5),
+                   ncol = 6, nrow = 2)
> 
> mE_example <- mainEff(BMB_example, fn = "fn_example",rangex =  rangex,xj = 3, N = 15, res = 4)
Warning in mainEff(BMB_example, fn = "fn_example", rangex = rangex, xj = 3,  :
  The tgp package is required
Error in LHS(res, r.x) : could not find function "LHS"
Calls: mainEff
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping vignette re-building
Packages suggested but not available for checking: 'rmarkdown', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
checkRd: (-1) bmr.Rd:172: Lost braces
   172 |    code{\link[stats]{formula}} interface instead, a regressor matrix may
       |        ^
Errors in running code in vignettes:
when running code in ‘bayesmeta.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder 'R.rsp' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘bayesmeta.Rmd’ using ‘UTF-8’... failed to complete the test
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'MCMCpack', 'FastGP', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot-traj.Rd:71: Lost braces; missing escapes or markup?
    71 | the plots are saved into directory {sim.dir}/predictions/migTrajectories.}
       |                                    ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rjags’

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: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'furrr', 'ggplot2', 'lubridate', 'MCMCpack', 'Rcpp',
  'tidyr', 'future', 'progressr', 'shiny', 'dygraphs', 'leaflet', 'sf',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'testthat', 'spelling', 'rmarkdown', 'ggforce',
  'RcppArmadillo', 'htmltools', 'shinythemes', 'DT', 'datamods',
  'viridis'

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

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: 'gplots', 'testthat'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'brms', 'ggplot2', 'dplyr', 'tidyr'

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

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

Packages suggested but not available for checking:
  'shiny', 'cyjShiny', 'qtl', 'qtlnet'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gsDesign', 'ggplot2', 'R2jags', 'rjags'

Package suggested but not available for checking: ‘testthat’

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

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown', 'vdiffr', 'ggplot2', 'patrick'

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

Packages suggested but not available for checking:
  'ggfortify', 'rmarkdown', 'rstan', 'rstanarm', 'rstantools',
  'scales', 'shinystan', 'testthat', 'vdiffr'

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

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

Package suggested but not available for checking: ‘wpp2015’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caTools', 'dplyr', 'ggplot2', 'ggridges', 'reshape2', 'tidyr',
  'ROCR', 'R2jags', 'runjags', 'rstanarm', 'rjags', 'MCMCpack', 'brms'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'forecast', 'scoringRules', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pgdraw’

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

Package suggested but not available for checking: ‘rmarkdown’

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

Package suggested but not available for checking: ‘roxygen2’

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

Package suggested but not available for checking: ‘roxygen2’

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

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

Package suggested but not available for checking: ‘testthat’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'janitor', 'dplyr', 'rstanarm', 'e1071', 'groupdata2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘splines2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'TeachingSampling'
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'dplyr', 'ggplot2',
  'lme4', 'RcppEigen', 'StanHeaders'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'xml2', 'igraph', 'tikzDevice', 'RcppArmadillo'

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

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

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

Package suggested but not available for checking: ‘rmarkdown’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesFactor', 'bayesplot', 'blavaan', 'bridgesampling', 'brms',
  'gamm4', 'ggdist', 'ggplot2', 'glmmTMB', 'lme4', 'mediation',
  'patchwork', 'posterior', 'RcppEigen', 'rmarkdown', 'rstan',
  'rstanarm', 'see', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rworldmap', 'wpp2015', 'ggplot2', 'sf', 'scales'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'extraDistr', 'bridgesampling', 'ggplot2'

Packages suggested but not available for checking:
  'scales', 'testthat', 'vdiffr', 'covr', 'rstan', 'rjags', 'runjags',
  'BayesFactor', 'rmarkdown'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tgp', 'BayesTree', 'bartMachine'
checkRd: (-1) BayesTreePrior.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:41: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BayesTree.Rcheck/00install.out’ for details.
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'faraway', 'hdi'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'rstan', 'StanHeaders', 'ggplot2', 'bayesplot', 'viridis',
  'reshape2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'BDgraph', 'ess', 'RcppArmadillo', 'RcppEigen'

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

Package suggested but not available for checking: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘R2BayesX’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BayesXsrc.Rcheck/00install.out’ for details.
Packages required but not available:
  'Rcpp', 'rstan', 'ggplot2', 'rstantools', 'RcppEigen', 'StanHeaders'

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggfortify', 'lme4', 'reshape2', 'scales',
  'tidyr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dataRetrieval', 'digest', 'dplyr', 'lubridate', 'memoise', 'pander',
  'plyr', 'readxl'

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

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

Package suggested but not available for checking: ‘testthat’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'future', 'glmnet', 'Rcpp', 'RcppAnnoy', 'reticulate', 'Rtsne',
  'Seurat', 'SeuratObject', 'uwot'

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

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

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) getOperatingSystem.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:30: Lost braces in \itemize; meant \describe ?
Running ‘run-all.R’ [0s/1s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'rstan', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'emdbook', 'rms', 'ggplot2', 'AICcmodavg', 'Hmisc', 'optimx',
  'testthat'
Note: skipping ‘mle2.Rnw’ due to unavailable dependencies: 'Hmisc'
Note: skipping ‘quasi.Rnw’ due to unavailable dependencies: 'AICcmodavg'
Packages required but not available: 'paradox', 'mlr3misc'

Packages suggested but not available for checking:
  'GenSA', 'nloptr', 'progressr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
Note: skipping ‘BBvignetteJSS.Stex’ due to unavailable dependencies:
  'Hmisc'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'mvnfast', 'greybox', 'glmnet'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'c3net', 'infotheo', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'glmnet', 'rmarkdown'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'lme4', 'MCMCpack', 'mixAK', 'Rcpp', 'Rmpfr',
  'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'crul', 'dbplyr', 'dplyr', 'leaflet', 'leaflet.extras', 'readr',
  'readxl', 'sf', 'xml2'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anomedOnlybic
> ### Title: The anomedOnlybic function
> ### Aliases: anomedOnlybic
> ### Keywords: anomedOnlybic
> 
> ### ** Examples
> 
> data(breastc)
> library(biclust)
Error in library(biclust) : there is no package called ‘biclust’
Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'MCMCvis', 'reshape2', 'rstan', 'scales', 'voi'

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

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

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

Package suggested but not available for checking: ‘testthat’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'bcdata', 'xml2'

Packages suggested but not available for checking:
  'future', 'future.apply', 'ggplot2', 'lwgeom', 'raster', 'terra',
  'rmarkdown', 'stars', 'testthat'

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

Packages suggested but not available for checking:
  'lubridate', 'digest', 'rmarkdown'

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

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

Package suggested but not available for checking: ‘rjags’

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

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Running ‘spelling.R’ [0s/0s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'CoordinateCleaner', 'dplyr', 'DT', 'fs', 'ggplot2', 'qs', 'readr',
  'rgnparser', 'rnaturalearth', 'sf', 'stringi', 'stringr', 'taxadb'

Packages suggested but not available for checking:
  'contentid', 'covr', 'cowplot', 'duckdb', 'raster', 'rmarkdown',
  'rvest', 'testthat', 'xml2'

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

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

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

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

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

Packages suggested but not available for checking:
  'ssgraph', 'huge', 'skimr', 'rmarkdown'

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

Package suggested but not available for checking: ‘rmarkdown’

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

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

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

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

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

Packages suggested but not available for checking:
  'cld2', 'rjson', 'rmarkdown', 'stringi', 'stringr', 'testthat',
  'tuber'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'is.R' is deprecated.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bdsmatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 17.0.6 (5)’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sqldf', 'plyr', 'taxize', 'treemap', 'ggplot2', 'sf'

Package suggested but not available for checking: ‘rinat’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'httpuv', 'stringr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppParallel', 'StanHeaders',
  'RcppEigen'

Packages suggested but not available for checking:
  'shiny', 'rmarkdown', 'pander', 'shinythemes', 'DT', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'shiny', 'shinydashboard', 'ggplot2', 'stringr', 'scales',
  'htmltools', 'httpuv', 'stringi', 'htmlwidgets', 'Rcpp', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'beautier', 'phangorn', 'readr', 'stringr', 'xml2'

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat', 'tracerer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Packages required but not available: 'ape', 'seqinr', 'stringr'

Packages suggested but not available for checking:
  'spelling', 'readr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘emdbook’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'visNetwork', 'dplyr', 'readr', 'stringr', 'shiny', 'DT', 'miniUI'

Packages suggested but not available for checking:
  'rmarkdown', 'biomaRt', 'GEOquery', 'htmltools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘testthat’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CoordinateCleaner', 'cowplot', 'dplyr', 'ggplot2', 'ggspatial',
  'igraph', 'lubridate', 'openxlsx', 'paletteer', 'readr',
  'rnaturalearth', 'sf', 'stringr'

Packages suggested but not available for checking:
  'bdc', 'classInt', 'ComplexHeatmap', 'devtools', 'emld', 'galah',
  'htmltools', 'htmlwidgets', 'janitor', 'leaflet', 'pkgdown',
  'plotly', 'prettydoc', 'rgnparser', 'rmarkdown', 'rmdformats',
  'rvest', 'terra', 'testthat', 'tidyr', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'tidyr', 'ggplot2',
  'cowplot', 'dplyr', 'odeGUTS', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nlsr', 'ggplot2', 'reshape2', 'optimx'

Packages suggested but not available for checking:
  'openxlsx', 'dplyr', 'tidyr', 'tidyverse', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BiasedUrn', 'data.tree', 'DiagrammeR', 'DiagrammeRsvg', 'ggplot2',
  'googlesheets4', 'rmdpartials', 'ufs', 'viridis'

Packages suggested but not available for checking:
  'htmltools', 'kableExtra', 'openxlsx', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'reshape2', 'ggplot2', 'ggfortify', 'future', 'future.apply',
  'GAS', 'ks', 'lubridate', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'raster', 'covr', 'rmarkdown', 'ggplot2', 'rasterVis',
  'stars', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'extraDistr', 'LambertW', 'Rcpp', 'rstan', 'rstantools',
  'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'benchmarkme', 'covr', 'DT', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'benchmarkmeData', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'covr', 'DT', 'ggplot2', 'RcppZiggurat', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggbeeswarm', 'ggplot2', 'ggridges', 'scales',
  'testthat', 'tidyr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘run-all.R’ [0s/0s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'benthos', 'readr', 'dplyr', 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'Rcpp', 'RcppParallel', 'rstan', 'rstantools',
  'scales', 'tidybayes', 'tidyr', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'bayesplot', 'covr', 'posterior', 'rmarkdown', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:14: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'readr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘jagsUI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'MCMCpack', 'Rglpk'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'Rcpp', 'RcppParallel', 'rstantools', 'rstan', 'scales',
  'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'rmarkdown', 'roxygen2', 'StanHeaders', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'gstat', 'spatstat.geom', 'ade4', 'leaflet',
  'leaflet.extras'
checkRd: (-1) headtail.Rd:28: Lost braces
    28 | Tries to find good methods of combining the two results according to {code{class(x)}}.
       |                                                                      ^
checkRd: (-1) headtail.Rd:28: Lost braces
    28 | Tries to find good methods of combining the two results according to {code{class(x)}}.
       |                                                                           ^
checkRd: (-1) logAxis.Rd:47: Lost braces; missing escapes or markup?
    47 | \item{expr}{Expression drawing over the ablines, like (points(x,y). Can be code within {braces}.}
       |                                                                                        ^
checkRd: (-1) smallPlot.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{expr}{expression creating a plot. Can be code within {braces}.}
       |                                                            ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'glmnet', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Package which this enhances but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggridges', 'patchwork', 'stringr'

Packages suggested but not available for checking: 'rmarkdown', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BiDAG', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'LambertW', 'dplyr', 'doRNG', 'recipes', 'butcher'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggplot2', 'scales', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'pheatmap', 'RcppEigen'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'shinydashboard', 'shinyWidgets', 'shinyBS',
  'shinyjs', 'tidyr', 'dplyr', 'readxl', 'ggplot2', 'DT', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘digest’

Packages suggested but not available for checking:
  'raster', 'DALEX', 'ggplot2', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'plotly', 'scales', 'pROC'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'mice', 'Amelia'
Running examples in ‘betaMC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MCMI
> ### Title: Generate the Sampling Distribution of Regression Parameters
> ###   Using the Monte Carlo Method for Data with Missing Values
> ### Aliases: MCMI
> ### Keywords: betaMC mc
> 
> ### ** Examples
> 
> # Data ---------------------------------------------------------------------
> data("nas1982", package = "betaMC")
> nas1982_missing <- mice::ampute(nas1982)$amp # data set with missing values
Error in loadNamespace(x) : there is no package called ‘mice’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ape', 'geometry', 'picante'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Note: skipping ‘betareg.Rnw’ due to unavailable dependencies: 'car'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/betategarch.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'forecast', 'rmarkdown', 'stringr', 'dygraphs',
  'shiny', 'miniUI', 'DT', 'digest', 'rjson', 'rvest', 'xml2',
  'lubridate', 'htmltools', 'dplyr', 'sqldf'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Ternary’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'forecast', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'strucchangeRcpp', 'forecast', 'Rcpp'

Packages suggested but not available for checking: 'stlplus', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BSDA', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'extraDistr', 'ergm', 'Bergm', 'QRM'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'doBy', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'dplyr'
Running examples in ‘bfsl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: augment.bfsl
> ### Title: Augment Data with Information from a bfsl Object
> ### Aliases: augment.bfsl
> 
> ### ** Examples
> 
> fit = bfsl(pearson_york_data)
> 
> augment(fit)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: augment ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'DescTools', 'sf'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xml2', 'rvest', 'janitor', 'tidyRSS', 'dplyr', 'sf', 'fs'

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', 'officer', 'plyr', 'runjags', 'rvg', 'scales'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'symDMatrix', 'bigmemory', 'synchronicity', 'ff'

Packages suggested but not available for checking:
  'lme4', 'SKAT', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'pryr', 'stringr', 'xml2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppDist'

Packages suggested but not available for checking:
  'devtools', 'testthat', 'covr', 'rmarkdown', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'testthat', 'covr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'rmarkdown', 'EasyMx', 'OpenMx', 'dplyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'qgraph', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'readr', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'miscTools', 'glmnet', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesm', 'Rcpp', 'RcppParallel', 'readxl', 'stochvol',
  'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bgw.Rcheck/00install.out’ for details.
Packages required but not available: 'prevtoinc', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘FrF2’
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'doRNG', 'R2jags'

Packages suggested but not available for checking:
  'doFuture', 'future', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'oro.nifti', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'bookdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bhpm.Rcheck/00install.out’ for details.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BHTSpack.Rcheck/00install.out’ for details.
Packages required but not available:
  'DT', 'rBiasCorrection', 'shiny', 'shinydashboard', 'shinyjs'

Packages suggested but not available for checking: 'lintr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BiasedUrn.Rcheck/00install.out’ for details.
Packages required but not available: 'dplyr', 'stringr', 'humaniformat'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'viridis', 'dendextend', 'randomcoloR', 'biclust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bibliometrix’
Packages required but not available:
  'dplyr', 'DT', 'FactoMineR', 'ggplot2', 'ggrepel', 'igraph',
  'plotly', 'openxlsx', 'readr', 'readxl', 'rscopus', 'shiny',
  'stringi', 'tidyr', 'tidytext'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'shinycssloaders', 'visNetwork',
  'wordcloud2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'stringr', 'yamlme'

Packages suggested but not available for checking:
  'covr', 'devtools', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggVennDiagram', 'shiny', 'UpSetR'

Packages suggested but not available for checking: 'DT', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running 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: 'rmarkdown', 'igraph'
Error(s) in re-building vignettes:
  ...
--- re-building ‘BiCausality_demo.Rmd’ using knitr

Quitting from lines 49-52 [unnamed-chunk-4] (BiCausality_demo.Rmd)
Error: processing vignette 'BiCausality_demo.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building ‘BiCausality_demo.Rmd’

SUMMARY: processing the following file failed:
  ‘BiCausality_demo.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'fields', 'DAAG', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'biclust', 'dplyr', 'phyclust'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'Rcpp', 'RBGL', 'pcalg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'crypto2', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'dplyr', 'ggplot2'
checkRd: (-1) BiDimRegression.Rd:29: Lost braces; missing escapes or markup?
    29 | \item \code{euclidean.df1, affine.df1} -  degrees of freedom of the nominator used for the F-statistics propagated by Nakaya (1997); df1 = p-2, with p is the number of elements  needed to calculate the referring model: p=4 for the Euclidean and p=6 for the affine geometry {Nakaya, 1997, Table 1}.
       |                                                                                                                                                                                                                                                                                  ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ape', 'sf', 'fasterize', 'raster', 'terra'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'mirt', 'MplusAutomation'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'alpaca', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'miceadds', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'lavaan.survey', 'survey', 'TAM'

Packages which this enhances but not available for checking:
  'Hmisc', 'intsvy', 'LSAmitR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fMultivar’

Packages suggested but not available for checking: 'igraph', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bigmemory', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Packages required but not available: 'bigmemory', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rmpfr', 'gmp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ff', 'ffbase', 'RSQLite', 'rjson'
Packages required but not available: 'FNN', 'rrcov'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘haplo.stats’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bigstatsr', 'furrr'

Packages suggested but not available for checking: 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fastDummies', 'future', 'future.apply', 'geos', 'sf', 'spatialreg',
  'spdep'

Packages suggested but not available for checking:
  'bookdown', 'INLA', 'rmarkdown', 'testthat', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘fields’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'bigmemory', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'glmnet', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘solartime’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Package suggested but not available for checking: ‘RSQLite’
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
Packages required but not available: 'ggplot2', 'plotly', 'scales'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'shiny', 'DT'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'bigmemory', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rcbalance', 'plyr', 'mvnfast'

Packages suggested but not available for checking: 'optmatch', 'rrelaxiv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

Packages which this enhances but not available for checking:
  'biganalytics', 'bigtabulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘bigmemory’
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bignum.Rcheck/00install.out’ for details.
Package required but not available: ‘flock’

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CompQuadForm’

Packages suggested but not available for checking: 'rmarkdown', 'SKAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'spelling', 'testthat', 'covr', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'clock', 'gargle'

Packages suggested but not available for checking:
  'covr', 'dbplyr', 'dplyr', 'readr', 'testthat', 'wk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘JuliaCall’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigstatsr', 'bigparallelr', 'bigsparser', 'bigreadr', 'bigutilsr',
  'doRNG', 'ggplot2', 'Rcpp', 'runonce', 'RcppArmadillo', 'rmio',
  'roptim'

Packages suggested but not available for checking:
  'bindata', 'covr', 'dbplyr', 'dplyr', 'gaston', 'Hmisc', 'pcadapt',
  'RSpectra', 'RSQLite', 'spelling', 'testthat', 'xgboost'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'rmio', 'RcppEigen'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'bigparallelr', 'cowplot', 'ggplot2', 'Rcpp', 'rmio', 'RSpectra',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'bigmemory', 'bigreadr', 'covr', 'dplyr', 'glmnet', 'ModelMetrics',
  'plotly', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bigmemory', 'RcppEigen'

Packages suggested but not available for checking:
  'devtools', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'bigmemory'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bigmemory', 'biganalytics', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'dplyr', 'ggplot2', 'tidyr', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigparallelr', 'nabor', 'Rcpp', 'RSpectra'

Packages suggested but not available for checking:
  'covr', 'Gmedian', 'rrcov', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppEigen'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'htmlwidgets', 'htmltools', 'ggplot2', 'scales', 'shiny'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplyr’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'digest', 'snakecase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'digest', 'prodlim'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'lhs', 'nloptr', 'GPfit', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fastGHQuad', 'Rcpp'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
Package required but not available: ‘e1071’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘dplyr’
Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'ggplot2', 'tidyr'
Package required but not available: ‘gplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'partitions', 'rBeta2009', 'Rcpp', 'scales',
  'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘partitions’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'xml2', 'semver'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rmarkdown', 'correlbinom'
Running examples in ‘binomialRF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binomialRF
> ### Title: random forest feature selection based on binomial exact test
> ### Aliases: binomialRF
> 
> ### ** Examples
> 
> set.seed(324)
> 
> ###############################
> ### Generate simulation data
> ###############################
> 
> X = matrix(rnorm(1000), ncol=10)
> trueBeta= c(rep(10,5), rep(0,5))
> z = 1 + X %*% trueBeta
> pr = 1/(1+exp(-z))
> y = as.factor(rbinom(100,1,pr))
> 
> ###############################
> ### Run binomialRF
> ###############################
> require(correlbinom)
Loading required package: correlbinom
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘correlbinom’
> 
> rho = 0.33
> ntrees = 250
> cbinom = correlbinom(rho, successprob =  calculateBinomialP(10, .5), trials = ntrees, 
+                                precision = 1024, model = 'kuk')
Error in correlbinom(rho, successprob = calculateBinomialP(10, 0.5), trials = ntrees,  : 
  could not find function "correlbinom"
Execution halted
Package required but not available: ‘pheatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
checkRd: (-1) binom.confint.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:45: Lost braces in \itemize; meant \describe ?
Running examples in ‘binom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binom.bayes
> ### Title: Binomial confidence intervals using Bayesian inference
> ### Aliases: binom.bayes binom.bayes.densityplot
> ### Keywords: univar htest models
> 
> ### ** Examples
> 
> # Example using highest probability density.
> hpd <- binom.bayes(
+   x = 0:10, n = 10, type = "highest", conf.level = 0.8, tol = 1e-9)
> print(hpd)
   method  x  n shape1 shape2       mean       lower     upper sig
1   bayes  0 10    0.5   10.5 0.04545455 0.000000000 0.0769566 0.2
2   bayes  1 10    1.5    9.5 0.13636364 0.003771457 0.2145408 0.2
3   bayes  2 10    2.5    8.5 0.22727273 0.053633312 0.3494770 0.2
4   bayes  3 10    3.5    7.5 0.31818182 0.127646004 0.4728042 0.2
5   bayes  4 10    4.5    6.5 0.40909091 0.214091147 0.5858428 0.2
6   bayes  5 10    5.5    5.5 0.50000000 0.309892028 0.6901080 0.2
7   bayes  6 10    6.5    4.5 0.59090909 0.414157185 0.7859089 0.2
8   bayes  7 10    7.5    3.5 0.68181818 0.527195809 0.8723540 0.2
9   bayes  8 10    8.5    2.5 0.77272727 0.650522982 0.9463667 0.2
10  bayes  9 10    9.5    1.5 0.86363636 0.785459228 0.9962285 0.2
11  bayes 10 10   10.5    0.5 0.95454545 0.923043403 1.0000000 0.2
> binom.bayes.densityplot(hpd)
Loading required namespace: ggplot2
Failed with error:  ‘there is no package called ‘ggplot2’’
Error in binom.bayes.densityplot(hpd) : 
  requireNamespace("ggplot2") is not TRUE
Calls: binom.bayes.densityplot -> stopifnot
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'hedgehog'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/binpackr.Rcheck/00install.out’ for details.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'covr', 'penaltyLearning', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'spatstat', 'spatstat.model', 'spatstat.geom',
  'spatstat.random', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'BAMMtools'
'LazyData' is specified without a 'data' directory
Running examples in ‘binst-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_jenksbreaks
> ### Title: Create Jenks breaks
> ### Aliases: create_jenksbreaks
> 
> ### ** Examples
> 
> jenks_breaks <- create_breaks(1:10, method="jenks")
Error in create_jenksbreaks(x, control = control) : 
  Please install BAMMtools: install.packages('BAMMtools')
Calls: create_breaks -> create_jenksbreaks
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'rstan', 'dplyr', 'stringi', 'rstantools', 'RcppEigen',
  'RcppParallel', 'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'RcppParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'igraph', 'bigmemory', 'rmarkdown', 'testthat', 'msa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmltools', 'Rcpp', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'htmlwidgets', 'plyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'terra', 'ggplot2', 'reshape2', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'testthat', 'rmarkdown'
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'rgl', 'e1071', 'pROC', 'ROCR', 'FSelector'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'digest', 'jsonvalidate', 'stringr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'ggplot2'

Packages suggested but not available for checking:
  'vegan3d', 'rgl', 'car', 'effects', 'dismo', 'raster', 'terra',
  'maxlike', 'gbm', 'kernlab', 'e1071', 'glmnet', 'geosphere',
  'ENMeval', 'red', 'igraph', 'maxnet', 'readxl', 'dplyr', 'sf',
  'blockCV', 'envirem', 'concaveman'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bsplus', 'dplyr', 'ggplot2', 'maxLik', 'mixtools', 'rhandsontable',
  'rmarkdown', 'shiny', 'shinydashboard', 'shinyWidgets', 'tidyr',
  'golem'

Packages suggested but not available for checking:
  'testthat', 'covr', 'kableExtra', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ecodist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘biogas_quick_start.Rnw’ using knitr

Quitting from lines 263-268 [unnamed-chunk-7] (biogas_quick_start.Rnw)
Error: processing vignette 'biogas_quick_start.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘biogas_quick_start.Rnw’

--- re-building ‘calcBgMan_function.Rnw’ using knitr

Quitting from lines 180-187 [unnamed-chunk-6] (calcBgMan_function.Rnw)
Error: processing vignette 'calcBgMan_function.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘calcBgMan_function.Rnw’

--- re-building ‘calcBgVol_function.Rnw’ using knitr

Quitting from lines 145-152 [unnamed-chunk-5] (calcBgVol_function.Rnw)
Error: processing vignette 'calcBgVol_function.Rnw' failed with diagnostics:
there is no package called 'ggplot2'
--- failed re-building ‘calcBgVol_function.Rnw’

--- re-building ‘predBg_function.Rnw’ using knitr
--- finished re-building ‘predBg_function.Rnw’

SUMMARY: processing the following files failed:
  ‘biogas_quick_start.Rnw’ ‘calcBgMan_function.Rnw’
  ‘calcBgVol_function.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘spatstat.geom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘partitions’

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', 'FME', 'ggplot2', 'cowplot', 'lamW', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EBImage’

Packages suggested but not available for checking:
  'rmarkdown', 'fs', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'FME', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'edgeR', 'wordcloud'

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: 'Rcpp', 'dplyr', 'igraph'

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xml2', 'memoise'

Packages suggested but not available for checking:
  'testthat', 'lintr', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'WGCNA', 'mlr3', 'ggsci', 'ROCR', 'caret', 'ggplot2', 'ggpubr',
  'viridis', 'ggthemes', 'ggstatsplot', 'htmlwidgets', 'jiebaR',
  'mlr3verse', 'uwot', 'wordcloud2', 'intergraph', 'igraph',
  'ggnetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'biomaRt', 'dplyr', 'readr', 'downloader', 'stringr', 'philentropy',
  'fs'

Packages suggested but not available for checking:
  'rmarkdown', 'devtools', 'testthat', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'terra'

Packages suggested but not available for checking:
  'rmarkdown', 'prettydoc', 'testthat', 'geodata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'farver', 'ggplot2', 'scales', 'stringi'

Packages suggested but not available for checking:
  'covr', 'mockery', 'rmarkdown', 'testthat', 'vdiffr'

Packages which this enhances but not available for checking:
  'asreml', 'ARTool', 'lme4', 'sommer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'terra', 'reshape', 'reshape2', 'ggplot2', 'gbm', 'xgboost',
  'maxnet', 'pROC', 'dplyr'

Packages suggested but not available for checking:
  'Hmisc', 'car', 'caret', 'dismo', 'ENMeval', 'raster', 'ggpubr',
  'testthat', 'tidyterra', 'ggtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) simulation.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:60-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulation.Rd:65: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'dplyr', 'fields', 'frictionless', 'ggplot2', 'lubridate', 'lutz',
  'raster', 'readr', 'rhdf5', 'suntools', 'tidyr', 'viridis'

Packages suggested but not available for checking:
  'aws.s3', 'ggspatial', 'prettymapr', 'rmarkdown', 'rosm', 'sf',
  'testthat', 'vdiffr', 'vol2birdR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'bipartite', 'dbscan', 'fastcluster', 'ggplot2', 'igraph',
  'rmarkdown', 'sf', 'tidyr', 'Rcpp'

Packages suggested but not available for checking:
  'ade4', 'dplyr', 'rnaturalearth', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'
Packages required but not available: 'bio3d', 'bigmemory', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'amap', 'e1071', 'scales', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'energy', 'fda.usc', 'parallelDist', 'osqp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'dplyr', 'stringi', 'stringr', 'readr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'ggplot2', 'scales'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'devtools', 'glmnet', 'plsRcox', 'pROC', 'survAUC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'bshazard', 'rstpm2', 'Epi', 'dplyr'
Running examples in ‘biostat3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lincom
> ### Title: Linear combination of regression parameters.
> ### Aliases: lincom
> 
> ### ** Examples
> 
>   fit <- glm(chd ~ hieng*job + offset(log(y)), data=diet, family=poisson)
>   lincom(fit, c("hienghigh+hienghigh:jobconductor",
+                 "hienghigh+hienghigh:jobbank"),
+          eform=TRUE)
Loading required namespace: car
Failed with error:  ‘there is no package called ‘car’’
Error in lincom(fit, c("hienghigh+hienghigh:jobconductor", "hienghigh+hienghigh:jobbank"),  : 
  Install the 'car' package to use the lincom function
Execution halted
Package required but not available: ‘learnr’

Packages suggested but not available for checking:
  'ggplot2', 'car', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'afex', 'cowplot', 'dplyr', 'ggh4x', 'ggplot2', 'ggstance',
  'MCMCglmm', 'openxlsx', 'plyr', 'reportRmd', 'rstatix', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running 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:
  'soilphysics', 'SpatialEpi', 'rmarkdown'
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'biomaRt', 'svglite'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'r2d3', 'dplyr', 'tidyr', 'stringr', 'downloader'

Packages suggested but not available for checking: 'bipartite', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rjags', 'dplyr'

Packages suggested but not available for checking:
  'dclone', 'mice', 'micemd', 'miceadds', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'matlib', 'rgl', 'shapes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'geosphere', 'ks', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'suntools', 'reshape2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'classInt', 'ggplot2'

Packages suggested but not available for checking:
  'covr', 'cowplot', 'rmarkdown', 'sf', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GOSemSim', 'AnnotationDbi'

Packages suggested but not available for checking: 'GO.db', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'spdep', 'spatialreg', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking: 'testthat', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Seurat', 'plyr', 'rmarkdown', 'testthat'
Running examples in ‘BisqueRNA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MarkerBasedDecomposition
> ### Title: Performs marker-based decomposition of bulk expression using
> ###   marker genes
> ### Aliases: MarkerBasedDecomposition
> 
> ### ** Examples
> 
> library(Biobase)
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> sim.data <- SimulateData(n.ind=10, n.genes=100, n.cells=100,
+                          cell.types=c("Neurons", "Astrocytes", "Microglia"),
+                          avg.props=c(.5, .3, .2))
Error in loadNamespace(x) : there is no package called ‘plyr’
Calls: SimulateData ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'IHW', 'testthat'
Packages required but not available:
  'rstantools', 'Rcpp', 'rstan', 'dplyr', 'future', 'tidyr',
  'RcppEigen', 'RcppParallel', 'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                               ^
checkRd: (-1) keypos.rd:27: Lost braces
    27 |   an integer vector of the same length as code{x} containing positions relativ to code{sort(unique(x), na.last=FALSE)}
       |                                                                                       ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ape', 'phytools', 'xml2'

Package suggested but not available for checking: ‘mvMORPH’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'digest', 'dplyr', 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'httptest', 'rmarkdown', 'testthat', 'tidyquant'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'rmarkdown', 'ff'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Errors in running code in vignettes:
when running code in ‘bit-demo.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘bit-performance.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘bit-usage.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘bit-demo.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘bit-performance.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘bit-usage.Rmd’ using ‘UTF-8’... failed to complete the test
Package suggested but not available for checking: ‘BoolNet’
Packages suggested but not available for checking:
  'ragg', 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'classInt', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'dplyr', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘mrfDepth’
Packages required but not available: 'fields', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'RQuantLib', 'testthat', 'covr', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running 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: ‘DHARMa’

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bkmr', 'future', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'fields', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'torch', 'R6P', 'ggplot2', 'ggmap'

Packages suggested but not available for checking: 'rmarkdown', 'R.rsp'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'R.rsp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geometry', 'spaMM', 'Rcpp', 'nloptr', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'minqa', 'lbfgsb3c', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Argument items with no description in Rd file 'ONA_compiled.Rd':
  ‘ATN’
Packages required but not available:
  'readr', 'dplyr', 'lubridate', 'tidyr', 'raster', 'sf',
  'exactextractr', 'stringr'

Packages suggested but not available for checking: 'geodata', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'LaF', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'ggExtra'
Packages required but not available:
  'ggplot2', 'stringr', 'jmvcore', 'rmarkdown'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSpectra’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'digest', 'dplyr', 'fs', 'htmltools', 'rmarkdown', 'stringr'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'testthat', 'spelling', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'digest', 'gWidgets2', 'gWidgets2tcltk', 'plot3Drgl', 'rgl', 'ergm',
  'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'nonnest2', 'rstan', 'rstantools', 'RcppParallel',
  'bayesplot', 'future.apply', 'StanHeaders', 'RcppEigen'

Packages suggested but not available for checking:
  'runjags', 'rjags', 'cmdstanr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fMultivar', 'fPortfolio', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rtkore', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'Rcpp'

Packages suggested but not available for checking:
  'terra', 'ggplot2', 'cowplot', 'automap', 'shiny', 'tmap', 'biomod2',
  'gstat', 'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'glmnetcr', 'pryr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'DT', 'htmlwidgets', 'igraph', 'intergraph', 'shinybusy',
  'shinyjs', 'shinythemes', 'visNetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doRNG’
Packages required but not available: 'Rcpp', 'digest', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'PolynomF'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'nbpMatching', 'RItools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'collapse', 'dplyr', 'ggplot2', 'ks'

Packages suggested but not available for checking:
  'devtools', 'questionr', 'reldist', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bookdown', 'htmltools', 'httpuv', 'later', 'rmarkdown', 'servr'

Packages suggested but not available for checking:
  'miniUI', 'shiny', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘maxLik’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'ggplot2', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat', 'vdiffr', 'xplorerr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rjags', 'openxlsx', 'reshape2', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable',
  'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable',
  'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'RSQLite', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'stringr'

Packages suggested but not available for checking: 'testthat', 'stringi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvnfast', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'janitor', 'leaflet', 'lubridate', 'readr', 'sf', 'stringr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'partitions', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rrcov’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Packages required but not available: 'Amelia', 'sem'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Amelia', 'sem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'forecast', 'ggplot2', 'rstan', 'rstantools', 'RcppParallel',
  'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'edstan', 'ggplot2',
  'GGUM', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BDgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'RcppParallel', 'rstan', 'rstantools',
  'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'qgraph', 'rmarkdown', 'reshape2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'xml2', 'rvest'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'MCMCpack', 'multicool'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'ggplot2', 'bayesplot'

Packages suggested but not available for checking:
  'reshape2', 'bridgesampling', 'testthat', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'spTimer', 'ggplot2', 'rstan', 'rstantools', 'spBayes',
  'CARBayes', 'CARBayesST', 'spTDyn', 'MCMCpack', 'inlabru', 'ggpubr',
  'RcppEigen', 'StanHeaders', 'RcppParallel'

Packages suggested but not available for checking:
  'INLA', 'extraDistr', 'cowplot', 'ggrepel', 'sf', 'rmarkdown',
  'testthat', 'ggspatial', 'interp', 'tidyr', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MCMCpack', 'ks', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘partitions’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BiDAG', 'RBGL', 'gRbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'janitor', 'lubridate', 'readr', 'readxl', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'np', 'dplyr', 'factormodel'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'igraph', 'gRbase', 'gRain', 'ROCR', 'Rmpfr', 'gmp'
Running examples in ‘bnlearn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arc.strength
> ### Title: Measure arc strength
> ### Aliases: arc.strength boot.strength custom.strength bf.strength
> ###   mean.bn.strength averaged.network inclusion.threshold
> ### Keywords: network scores independence tests structure learning
> 
> ### ** Examples
> 
> data(learning.test)
> dag = hc(learning.test)
> arc.strength(dag, learning.test)
  from to   strength
1    A  B -1153.8796
2    A  D -1938.9499
3    C  D  -823.7605
4    B  E  -720.8266
5    F  E  -549.2300
> 
> ## Not run: 
> ##D arcs = boot.strength(learning.test, algorithm = "hc")
> ##D arcs[(arcs$strength > 0.85) & (arcs$direction >= 0.5), ]
> ##D averaged.network(arcs)
> ##D 
> ##D start = random.graph(nodes = names(learning.test), num = 50)
> ##D netlist = lapply(start, function(net) {
> ##D   hc(learning.test, score = "bde", iss = 10, start = net) })
> ##D arcs = custom.strength(netlist, nodes = names(learning.test),
> ##D          cpdag = FALSE)
> ##D arcs[(arcs$strength > 0.85) & (arcs$direction >= 0.5), ]
> ##D modelstring(averaged.network(arcs))
> ## End(Not run)
> 
> bf.strength(dag, learning.test, score = "bds", prior = "marginal")
Loading required namespace: Rmpfr
Failed with error:  ‘there is no package called ‘Rmpfr’’
Error in check.and.load.package("Rmpfr") : 
  this function requires the Rmpfr package.
Calls: bf.strength -> check.and.load.package
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rjags', 'ggplot2', 'igraph'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'gRain', 'gRbase', 'qgraph', 'reshape2', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'prodlim', 'pec', 'Rcpp'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fastDummies', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr', 'viridis'

Packages suggested but not available for checking:
  'GreedyEPL', 'Rmpfr', 'gmp', 'rmarkdown', 'testthat', 'BNPmix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'Rcpp', 'ggpubr', 'RcppArmadillo', 'RcppDist'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

Packages suggested but not available for checking:
  'popkin', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'threejs', 'cubature', 'plyr'

Package suggested but not available for checking: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Packages suggested but not available for checking: 'qgraph', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'visNetwork', 'igraph', 'shiny', 'caret', 'e1071'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ggplot2', 'cytofan', 'dplyr', 'reshape2', 'rmarkdown'
checkRd: (-1) refAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) refAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:13-14: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'ranger', 'gbm', 'opera'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xml2', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Extractor.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:19: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘copula’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'Hmisc', 'lubridate', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'readr', 'tidyr', 'rvest', 'xml2'

Packages suggested but not available for checking: 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'future.apply', 'ggplot2', 'glmnet', 'progressr'

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xml2', 'crul', 'stringi'

Packages suggested but not available for checking:
  'sangerseqR', 'testthat', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'bnstruct'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'imager', 'HelpersMG', 'rmarkdown', 'shiny'

Packages suggested but not available for checking: 'ijtiff', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'parsnip', 'dials', 'dplyr'

Packages suggested but not available for checking:
  'covr', 'lightgbm', 'modeldata', 'rmarkdown', 'rsample', 'testthat',
  'tune'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppNumerical', 'RcppEigen'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmltools', 'rmarkdown', 'jquerylib'

Packages suggested but not available for checking:
  'bslib', 'downlit', 'htmlwidgets', 'miniUI', 'rsconnect', 'servr',
  'shiny', 'tufte', 'xml2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BoolNet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Boom.Rcheck/00install.out’ for details.
Package required but not available: ‘Boom’

Packages suggested but not available for checking: 'testthat', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rglpk', 'dplyr', 'MLmetrics'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘randomForestSRC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fpc', 'plyr', 'dplyr', 'igraph', 'ggplot2', 'intergraph', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ARDL', 'dplyr', 'stringr', 'usethis', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rmarkdown', 'reshape2', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'readxl'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'covr', 'roxygen2', 'pkgdown', 'devtools', 'mockery',
  'rmarkdown'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rmarkdown’

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: ‘mice’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'igraph', 'IsingFit', 'qgraph', 'dplyr', 'tidyr',
  'IsingSampler', 'mgm', 'NetworkToolbox', 'networktools'

Packages suggested but not available for checking:
  'GGMncv', 'BDgraph', 'graphicalVAR', 'relaimpo', 'huge'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plsRglm', 'bipartite'

Packages suggested but not available for checking: 'prettydoc', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'lme4', 'rms', 'gt', 'flextable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) select_Uc.Rd:16: Lost braces
    16 | function /code{ppBS_srs()}.
       |               ^
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'qvalue', 'testthat'
Package unavailable to check Rd xrefs: ‘qvalue’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'RcppArmadillo', 'RcppThread'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'npboottprm', 'shiny', 'shinyjs', 'shinythemes'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fishMod', 'R2jags', 'reshape2'

Package suggested but not available for checking: ‘mvabund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BART', 'Rcpp'

Packages suggested but not available for checking: 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

Packages suggested but not available for checking: 'testthat', 'xgboost'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'cplexAPI', 'testthat', 'glmnet', 'rmarkdown', 'ggplot2', 'ggpubr',
  'dplyr', 'kableExtra', 'devtools', 'BiocStyle', 'bestsubset'
Documented arguments not in \usage in Rd file 'InternalFunctions.Rd':
  ‘metric’ ‘matrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ape', 'RSQLite', 'phangorn'

Packages suggested but not available for checking: 'prettydoc', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

Packages suggested but not available for checking:
  'testthat', 'covr', 'digest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'terra', 'ggplot2', 'igraph', 'fields', 'rgeoda', 'scales'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spelling', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'imager', 'gplots'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'latticeExtra', 'e1071'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qicharts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'crosstalk', 'ggplot2', 'htmlwidgets', 'htmltools', 'plotly'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'devtools', 'rmarkdown', 'roxygen2', 'shiny', 'stringr', 'testthat'
Documented arguments not in \usage in Rd file 'info.Rd':
  ‘mod_spec’ ‘pkg_spec’

Documented arguments not in \usage in Rd file 'path.Rd':
  ‘args’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Needed for subshells openend in tests, and does no harm otherwise.
  > # See <https://github.com/hadley/testthat/issues/144> for details.
  > Sys.setenv(R_TESTS = '')
  > testthat::test_check('box')
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'dplyr', 'digest', 'fs', 'httpuv', 'rio', 'stringr'

Packages suggested but not available for checking:
  'conflicted', 'gargle', 'rmarkdown', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'rmarkdown', 'shiny', 'testthat', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mcmcse', 'Rcpp', 'fabMix', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'DiagrammeRsvg', 'dplyr', 'htmltools', 'htmlwidgets',
  'rvest', 'tidyr', 'DT', 'huxtable', 'stringr', 'readr', 'xml2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'xml2'

Packages suggested but not available for checking:
  'shiny', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'haven', 'RcppArmadillo'

Packages suggested but not available for checking: 'qpdf', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'tidyr', 'lubridate', 'ggplot2', 'cowplot'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'furrr', 'Rcpp', 'rstan', 'stringr', 'RcppEigen',
  'RcppParallel', 'StanHeaders'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘NPflow’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘survminer’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'V8'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fbst', 'extraDistr'

Packages suggested but not available for checking: 'rmarkdown', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'devtools', 'dplyr', 'ggplot2', 'hunspell', 'quarto', 'rmarkdown',
  'tidyr'

Packages suggested but not available for checking:
  'broom', 'ggfortify', 'installr', 'rstatix', 'spelling', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'Hmisc', 'RGtk2', 'ade4', 'cairoDevice', 'car', 'ggplot2', 'ggrepel',
  'mediation', 'oro.nifti', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CCA', 'kernlab', 'rgl', 'brainR', 'oro.nifti'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgl', 'oro.nifti'

Package suggested but not available for checking: ‘servr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Branching.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'QCA', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gmp', 'kantorovich'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'readxl', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'GJRM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'arrow', 'lobstr'

Packages suggested but not available for checking: 'testthat', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tidyverse', 'rmarkdown'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'readr', 'stringr'

Packages suggested but not available for checking:
  'spelling', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'lme4', 'phyloseq'

Packages suggested but not available for checking:
  'devtools', 'plyr', 'rmarkdown', 'testthat', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'rmarkdown', 'e1071', 'kernlab', 'xgboost', 'caret', 'DALEX',
  'ranger', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'Rcpp', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggfittext', 'ggplot2', 'broom', 'readr', 'readxl',
  'stringr', 'tidyr', 'xml2'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'breathteststan', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'rstan', 'rstantools', 'stringr', 'tidyr',
  'breathtestcore', 'StanHeaders', 'RcppEigen'

Packages suggested but not available for checking:
  'ggplot2', 'shinystan', 'igraph', 'bayesplot', 'testthat', 'covr',
  'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'detectseparation', 'rmarkdown', 'covr'
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) brglm.Rd:173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:174: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:175-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:181-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:183-184: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:58: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'piggyback'

Packages suggested but not available for checking: 'DT', 'ggplot2', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'reshape2', 'ggplot2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'shiny', 'shinydashboard', 'plotly', 'BSDA'

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', 'patchwork', 'tidyr', 'ggplot2', 'ggedit',
  'kableExtra', 'pdftools', 'scales', 'stringr'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'scales'

Packages suggested but not available for checking:
  'testthat', 'Rcpp', 'RcppEigen', 'R2jags', 'rjags', 'runjags',
  'rmarkdown', 'R.rsp', 'BayesFactor', 'rstan', 'rstanarm', 'nimble',
  'MCMCpack'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘splines2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', '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:
  'ggplot2', 'rmarkdown', 'pander', 'lubridate', 'GGally', 'patchwork',
  'scales'

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: 'covr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

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: 'RANN', 'rdist'

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:
  'fs', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'brms', 'Rcpp', 'posterior', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'brms', 'dplyr', 'ggplot2', 'ggridges', 'posterior', 'tidyr',
  'trialr'

Packages suggested but not available for checking:
  'Rcpp', 'RcppEigen', 'RcppParallel', 'rmarkdown', 'rstan',
  'StanHeaders', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'ggplot2', 'posterior', 'rstantools', 'bayesplot',
  'shinystan', 'bridgesampling', 'future'

Packages suggested but not available for checking:
  'testthat', 'cmdstanr', 'projpred', 'rtdists', 'extraDistr', 'mice',
  'spdep', 'lme4', 'MCMCglmm', 'splines2', 'ape', 'arm', 'digest',
  'R.rsp', 'shiny', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'cubature', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Cyclops’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lme4', 'tidyr'

Packages suggested but not available for checking:
  'bookdown', 'ggplot2', 'mice', 'plyr', 'svglite', 'testthat',
  'rmarkdown'

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', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'labelled', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'covr', 'effects', 'fixest', 'geepack',
  'ggplot2', 'ggstats', 'glmmTMB', 'gt', 'gtsummary', 'lme4', 'logitr',
  'marginaleffects', 'mice', 'multgee', 'parsnip', 'patchwork', 'plm',
  'rmarkdown', 'rstanarm', 'scales', 'spelling', 'survey', 'testthat',
  'tidycmprsk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom', 'dplyr', 'stringr', 'tidyr', 'furrr'

Packages suggested but not available for checking:
  'brms', 'dotwhisker', 'testthat', 'ggplot2', 'glmmADMB', 'glmmTMB',
  'lmerTest', 'lme4', 'MCMCglmm', 'pander', 'pbkrtest', 'rstan',
  'rstanarm', 'rstantools', 'R2jags', 'TMB', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'AER', 'binGroup', 'btergm', 'car', 'caret', 'covr', 'drc', 'e1071',
  'epiR', 'ergm', 'fixest', 'geepack', 'ggplot2', 'glmnet',
  'glmnetUtils', 'Hmisc', 'interp', 'joineRML', 'ks', 'Lahman', 'lme4',
  'mediation', 'mlogit', 'modeldata', 'modeltests', 'plm', 'rmarkdown',
  'robust', 'rsample', 'spdep', 'spatialreg', 'spelling', 'survey',
  'systemfit', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'spelling', 'R.rsp', 'rmarkdown', 'ggplot2'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Running ‘spelling.R’ [0s/1s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Errors in running code in vignettes:
when running code in ‘benchmarks.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder 'R.rsp' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘benchmarks.Rmd’ using ‘UTF-8’... failed to complete the test
Package required but not available: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'future', 'multidplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rio', 'plyr', 'dplyr', 'tidyr', 'stringr', 'ggplot2', 'afex',
  'mediation', 'interactions', 'jtools', 'lmerTest'

Packages suggested but not available for checking:
  'haven', 'readxl', 'openxlsx', 'cowplot', 'ggtext', 'see', 'car',
  'lme4', 'phia', 'BayesFactor', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'is.R' is deprecated.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BRugs.Rcheck/00install.out’ for details.
* used C compiler: ‘Debian clang version 17.0.6 (5)’
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
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'.
Found the following significant warnings:

  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'ggplot2', 'torch'

Packages suggested but not available for checking:
  'covr', 'modeldata', 'recipes', 'spelling', 'testthat', 'yardstick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'dplyr', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MCMCpack', 'blavaan', 'blme', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘htmltools’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr', 'bslib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'htmltools', 'fresh', 'waiter', 'httpuv', 'bslib'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'golem', 'DT', 'thematic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MCPAN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rjags', 'dplyr', 'ggplot2', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'webshot2'

Packages suggested but not available for checking:
  'rmarkdown', 'xml2', 'dplyr', 'readr', 'stringr', 'scales', 'shiny',
  'reactable', 'reactable.extras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘e1071’

Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘MfUSampler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Epi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘htmltools’

Packages suggested but not available for checking:
  'bslib', 'testthat', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'shiny'
Packages required but not available:
  'cowplot', 'tidyr', 'dplyr', 'ggplot2', 'ggpubr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'brms', 'rstan', 'dplyr', 'sitar'

Packages suggested but not available for checking:
  'bookdown', 'kableExtra', 'rmarkdown', 'spelling', 'Hmisc',
  'testthat', 'R.rsp', 'bayesplot', 'marginaleffects', 'future',
  'future.apply', 'ggplot2', 'jtools', 'patchwork', 'posterior',
  'tidyr', 'extraDistr'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fs', 'lubridate', 'stringi', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'httptest2', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cachem', 'htmltools', 'jquerylib', 'memoise', 'sass'

Packages suggested but not available for checking:
  'bsicons', 'fontawesome', 'ggplot2', 'rmarkdown', 'shiny',
  'testthat', 'thematic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'copula', 'Rcpp', 'doRNG', 'stringr', 'RcppArmadillo'

Package suggested but not available for checking: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘C50’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'glmnet', 'gplots', 'BayesGPfit', 'neurobase', 'oro.nifti',
  'ggplot2', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'arrApply', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmltools', 'lubridate', 'stringr', 'rmarkdown'

Packages suggested but not available for checking:
  'testthat', 'shiny', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘stochvol’
Running examples in ‘bsreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bm
> ### Title: Fit a Bayesian model
> ### Aliases: bm bm.formula bm.bm blm bslx bsar bsem bsdm bsdem bsv
> 
> ### ** Examples
> 
> N <- 100L
> beta <- 1:5
> X <- matrix(rnorm(N * 5), N, 5)
> y <- X %*% beta + rnorm(N)
> 
> bm(y ~ X, n_burn = 100, n_draw = 100)
Error: Package 'stochvol' required for this method.
Execution halted
Packages required but not available: 'fICA', 'JADE'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'diagis', 'dplyr', 'posterior', 'Rcpp', 'tidyr',
  'ramcmc', 'RcppArmadillo', 'sitmo'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'rmarkdown', 'ramcmc', 'sde', 'sitmo', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ClusterR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SpatialBSS', 'rSPDE'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phangorn’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gbm’

Packages suggested but not available for checking: 'hdi', 'pROC', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘extraDistr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BoomSpikeSlab', 'Boom'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GetoptLong', 'digest'

Packages suggested but not available for checking:
  'DT', 'shiny', 'shinyjqui', 'igraph', 'ggplot2', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppTN', 'stochvol', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (requireNamespace("BSW")) {
  +   library(BSW)
  +   library(testthat)
  +   test_check("BSW")
  + }
  Loading required namespace: BSW
  Loading required package: Matrix
  Loading required package: matrixStats
  Loading required package: quadprog
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'mapsf', 'Rcpp', 'sf', 'RcppParallel', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'ROCR', 'igraph'

Packages suggested but not available for checking:
  'fastglm', 'testthat', 'Bergm', 'RSiena', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'stringr', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘udpipe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'ggforce', 'plyr', 'reshape2', 'R2jags', 'scales'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'BTYD', 'bayesm'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown', 'lintr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'dplyr'

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘htmltools’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Amelia', 'mice'
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'plyr', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'gamm4', 'glmertree', 'glmmTMB', 'lmerTest', 'pbkrtest', 'rmarkdown',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'usethis', 'readr', 'stringr'

Packages suggested but not available for checking:
  'rmarkdown', 'roxygen2', 'testthat', 'spelling', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘digest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mpath', 'gbm', 'rms', 'bst'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'shiny', 'gprofiler2', 'edgeR', 'DESeq2', 'ggrepel',
  'ComplexHeatmap', 'shinyWidgets', 'shinyjqui', 'dplyr', 'ggforce',
  'noisyr', 'ggnewscale', 'ggrastr', 'GENIE3', 'visNetwork', 'DT',
  'scales', 'shinyjs', 'tidyr', 'shinyLP', 'UpSetR', 'stringr',
  'ggVennDiagram'

Packages suggested but not available for checking:
  'rmarkdown', 'shinythemes', 'AnnotationDbi', 'org.Hs.eg.db',
  'org.Mm.eg.db', 'readxl', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fs', 'googlesheets4', 'haven', 'inspectdf', 'labelled',
  'lubridate', 'openxlsx', 'readr', 'readxl', 'stringr'

Packages suggested but not available for checking: 'rmarkdown', '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: 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xml2', 'ggplot2', 'plyr', 'dplyr', 'reshape2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'Hmisc', 'rmarkdown'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'broom', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr', 'car', 'rsq'

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: 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bonsai', 'butcher', 'caret', 'covr', 'embed', 'keras', 'kernlab',
  'luz', 'modeldata', 'parsnip', 'recipes', 'rmarkdown', 'stacks',
  'tensorflow', 'testthat', 'torch', 'torchvision', 'uwot', 'vetiver',
  'workflows', 'xgboost'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'shiny', 'miniUI', 'tidyr', 'stringr', 'stringi',
  'lubridate', 'ggplot2'

Packages suggested but not available for checking:
  'covr', 'lintr', 'edeaR', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'edeaR', 'processcheckR', 'processmapR'

Packages suggested but not available for checking: 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plyr', 'reshape2', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'rvest', 'stringr', 'readr', 'openxlsx'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lubridate’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘kableExtra’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lobstr’

Packages suggested but not available for checking:
  'C50', 'caret', 'ClusterR', 'clustMixType', 'covr', 'dbarts',
  'ddalpha', 'dimRed', 'dplyr', 'e1071', 'flexsurv', 'fs', 'ipred',
  'kernlab', 'kknn', 'klaR', 'modeldata', 'nestedmodels', 'parsnip',
  'pkgload', 'ranger', 'RANN', 'recipes', 'rmarkdown', 'rsample',
  'RSpectra', 'sparklyr', 'testthat', 'tidyr', 'usethis', 'xgboost',
  'xrf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'lava', 'prodlim', 'riskRegression', 'scales',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'cvAUC', 'pROC', 'R.rsp', 'testthat'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package vignette without corresponding tangle output:
  ‘article.Rnw’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'tidyr', 'dplyr', 'posterior', 'bayesplot',
  'doRNG', 'RcppEigen'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'RcppEigen', 'RcppNumerical'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'e1071', 'stringi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'RcppEigen',
  'StanHeaders'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'memoise', 'Rcpp'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'igraph', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'tgp', 'penalized', 'penalizedSVM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/c212.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'e1071'
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'rvest', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'readr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'dplyr', 'viridis'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'igraph', 'plyr', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Cubist’

Packages suggested but not available for checking:
  'covr', 'modeldata', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plotly', 'ggforce', 'ggrepel', 'multichull'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fs', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fastmap’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘digest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Seurat', 'pheatmap', 'ROCR', 'reshape2', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dynlm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown', 'spelling'
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'RLRsim'

Package suggested but not available for checking: ‘gamm4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'classInt', 'FactoMineR', 'ggplot2', 'ggrepel', 'Hmisc', 'RcmdrMisc',
  'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'smoof', 'rmarkdown', 'car', 'dplyr', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ape', 'rmarkdown', 'taxize', 'dendextend', 'heatmaply', 'ggplot2',
  'plotly', 'DT', 'htmltools', 'htmlwidgets', 'pkgdown'

Packages suggested but not available for checking: 'AnnotationDbi', 'GO.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'cubature', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) calcUnique.Rd:24: Lost braces
    24 | functions, and often the /code{cut()} function are relatively slow when working with tens of millions of rows or more.
       |                               ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘lubridate’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'gggibbous', 'ggimage', 'ggplot2', 'suncalc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'suncalc', 'ggimage', 'gggibbous'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mice’

Packages suggested but not available for checking: 'missForest', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggpubr', 'Hmisc', 'rms', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘optimx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GPfit', 'kernlab'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Packages suggested but not available for checking: 'ReGenesees', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ggplot2', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'ggplot2', 'Hmisc', 'bookdown'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'pROC', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'survey', 'kableExtra', 'stringr', 'tidyr', 'haven'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'asciicast', 'covr', 'mockery', 'spelling', 'testthat'
Documented arguments not in \usage in Rd file 'get_result.Rd':
  ‘out’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'oce', 'stringr', 'scales'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'aroma.core', 'R.filesets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'digest', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'ExactMultinom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CAMAN.Rcheck/00install.out’ for details.
Packages required but not available: 'ggplot2', 'magick', 'svglite'

Packages suggested but not available for checking:
  'rmarkdown', 'ragg', 'covr', 'testthat', 'patchwork', 'dplyr',
  'systemfonts', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'Rcpp', 'shiny'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Seurat', 'org.Hs.eg.db', 'org.Dr.eg.db', 'org.Mm.eg.db',
  'AnnotationDbi', 'SeuratObject', 'edgeR'

Package suggested but not available for checking: ‘sctransform’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'ggplot2', 'tidyr'
Packages required but not available:
  'dplyr', 'fs', 'ggplot2', 'lubridate', 'readr', 'scales', 'stringr'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'spelling', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'plyr', 'readr'

Packages suggested but not available for checking:
  'devtools', 'pkgdown', 'rmarkdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'campsismod', 'digest', 'dplyr', 'ggplot2', 'furrr', 'future',
  'plyr', 'progressr', 'tidyr'

Packages suggested but not available for checking:
  'bookdown', 'devtools', 'mrgsolve', 'pkgdown', 'rmarkdown',
  'roxygen2', 'rxode2', 'stringr', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xml2’

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'rmapshaper', 'dplyr'

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'sf', 'ggrepel', 'dplyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'assertr', 'dplyr', 'future.apply', 'phyloregion', 'progressr'

Packages suggested but not available for checking:
  'rmarkdown', 'future', 'patchwork', 'testthat', 'stringr', 'covr',
  'picante', 'fs', 'readr', 'usethis', 'scales', 'colorBlindness'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'digest', 'dplyr'

Packages suggested but not available for checking:
  'ggplot2', 'leaflet', 'mapdeck', 'rmarkdown', 'readr', 'scales',
  'sf', 'geojsonsf', 'tidyr', 'lwgeom', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'stringr', 'BoutrosLab.plotting.general'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'systemfit', 'qvalue', 'reshape2', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'biogram', 'devtools', 'ranger', 'shiny', 'stringi', 'dplyr'

Packages suggested but not available for checking:
  'DT', 'ggplot2', 'pander', 'rmarkdown', 'shinythemes', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'gargle', 'lubridate', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'heplots'

Packages suggested but not available for checking: 'rgl', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FNN', 'fpc', 'bluster', 'igraph'

Packages suggested but not available for checking:
  'testthat', 'Seurat', 'scater', 'batchelor', 'scran', 'rmarkdown',
  'patchwork', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'fields', 'pheatmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rmarkdown’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'Hmisc', 'downloader'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'digest', 'dplyr', 'readr', 'xml2', 'rvest', 'stringr', 'RSQLite'

Packages suggested but not available for checking:
  'rmarkdown', 'scales', 'tidyr', 'ggplot2', 'dbplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'usethis'
Packages required but not available: 'htmlwidgets', 'htmltools'

Packages suggested but not available for checking:
  'shiny', 'dplyr', 'DT', 'readr', 'rmarkdown', 'stringr', 'testthat',
  'tidyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caTools', 'igraph', 'pheatmap', 'propagate', 'qtl', 'qtl2',
  'qtl2convert'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'readxl', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FME', 'survey', 'ggplot2', 'dplyr', 'tidyr', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'htmltools', 'shinyjs', 'shinyWidgets', 'shinydashboard',
  'shinydashboardPlus', 'shinyjqui', 'plotly', 'rintrojs',
  'shinycssloaders', 'visNetwork', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reticulate', 'doBy'

Packages suggested but not available for checking:
  'Ryacas', 'testthat', 'rmarkdown', 'magick', 'pdftools', 'qpdf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'stringr', 'RcppArmadillo'

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'CARBayesdata', 'dplyr', 'GGally', 'glmnet', 'igraph',
  'mapview', 'MCMCpack', 'sf', 'spam', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'CARBayesdata', 'dplyr', 'GGally', 'ggplot2', 'leaflet',
  'MCMCpack', 'sf', 'spam', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'details', 'httpuv', 'magick', 'RSelenium', 'wdman'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/carbondate.Rcheck/00install.out’ for details.
Packages required but not available: 'lme4', 'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgl’
checkRd: (-1) plot.ca.rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:66: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘car’
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) fitweibull.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'lutz', 'ggplot2', 'tidyr', 'dplyr', 'readr', 'lubridate',
  'stringr', 'broom', 'recipes', 'Hmisc', 'ggrepel'

Packages suggested but not available for checking:
  'kableExtra', 'plyr', 'rmarkdown', 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown', 'dplyr', 'ggplot2', 'spelling'
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'digest', 'plyr', 'caret'

Packages suggested but not available for checking:
  'caTools', 'testthat', 'lintr', 'glmnet', 'kernlab', 'e1071',
  'ipred', 'pROC', 'gbm', 'klaR', 'rmarkdown', 'usethis', 'sass'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'caret', 'dplyr'

Packages suggested but not available for checking: 'Cubist', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'e1071', 'ModelMetrics', 'plyr', 'pROC', 'recipes',
  'reshape2'

Packages suggested but not available for checking:
  'BradleyTerry2', 'covr', 'Cubist', 'dplyr', 'ipred', 'kernlab',
  'klaR', 'MLmetrics', 'RANN', 'rmarkdown', 'subselect', 'testthat',
  'themis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘roxygen2’
checkRd: (-1) build_for_cran.Rd:13: Lost braces
    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'igraph', 'ggraph', 'ggplot2', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'scales', 'patchwork'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders',
  'RcppParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arrangements', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Package suggested but not available for checking: ‘RSQLite’

Package which this enhances but not available for checking: ‘gplots’
Running examples in ‘caroline-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bestBy
> ### Title: Find the "best" record within subgroups of a dataframe.
> ### Aliases: bestBy
> 
> ### ** Examples
> 
> 
> blast.results <- data.frame(score=c(1,2,34,4,5,3,23), 
+                             query=c('z','x','y','z','x','y','z'), 
+                             target=c('a','b','c','d','e','f','g')
+                             )
> best.hits.R <- bestBy(blast.results, by='query', best='score', inverse=TRUE)
> best.hits.R
  score query target
y    34     y      c
z    23     z      g
x     5     x      e
> ## or using SQLite
> best.hits.sql <- bestBy(blast.results, by='query', best='score', inverse=TRUE, sql=TRUE)
Loading required namespace: RSQLite
Failed with error:  ‘there is no package called ‘RSQLite’’
Error in loadNamespace(x) : there is no package called ‘RSQLite’
Calls: bestBy ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'dplyr', 'tidyr', 'pander'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pbkrtest', 'lme4', 'scales'

Packages suggested but not available for checking:
  'alr4', 'effects', 'rgl', 'rio', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lobstr’

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'reshape2', 'sf', 'igraph'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'cartography'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'packcircles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: 'dplyr', 'sf'

Packages suggested but not available for checking:
  'ggplot2', 'rnaturalearth', 'rnaturalearthhires', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'classInt', 'raster', 'Rcpp', 'sf'

Packages suggested but not available for checking:
  'lwgeom', 'SpatialPosition', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gsheet', 'rvest', 'RJSONIO'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'animation', 'igraph', 'tnet'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fontawesome', 'htmltools', 'reactR', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'expsmooth', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'igraph'
Running examples in ‘CASCORE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SCORE
> ### Title: Spectral Clustering On Ratios-of-Eigenvectors.
> ### Aliases: SCORE
> 
> ### ** Examples
> 
> 
> # Simulate the Network
> n = 10; K = 2;
> theta = 0.4 + (0.45-0.05)*(seq(1:n)/n)^2; Theta = diag(theta);
> P  = matrix(c(0.8, 0.2, 0.2, 0.8), byrow = TRUE, nrow = K)
> set.seed(2022)
> l = sample(1:K, n, replace=TRUE); # node labels
> Pi = matrix(0, n, K) # label matrix
> for (k in 1:K){
+   Pi[l == k, k] = 1
+ }
> Omega = Theta %*% Pi %*% P %*% t(Pi) %*% Theta;
> Adj = matrix(runif(n*n, 0, 1), nrow = n);
> Adj = Omega - Adj;
> Adj = 1*(Adj >= 0)
> diag(Adj) = 0
> Adj[lower.tri(Adj)] = t(Adj)[lower.tri(Adj)]
> library(igraph)
Error in library(igraph) : there is no package called ‘igraph’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘copula’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rms', 'ranger', 'ggplot2', 'cowplot',
  'dplyr', 'tidyr', 'pryr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'covr', 'dplyr', 'glmnet', 'lubridate', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'bindata', 'copula', 'dplyr', 'extraDistr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'readr', 'rmarkdown', 'covr', 'badger', 'glmnet'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

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: 'rmarkdown', 'beepr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bipartite', 'reshape2', 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'rmarkdown', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'alphahull', 'interp', 'energy', 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'rmarkdown', 'GGally', 'tidyr', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RSpectra'

Packages suggested but not available for checking: 'nloptr', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'ggplot2', 'FNN', 'plyr', 'sf'

Packages suggested but not available for checking:
  'lubridate', 'mapview', 'rmarkdown', 'scales', 'viridis', 'stars',
  'terra', 'rnaturalearth', 'twosamples', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'dplyr', 'rmarkdown', 'testthat', 'tidyr'
Running examples in ‘cat2cat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cat2cat_agg
> ### Title: Manual mapping for an aggregated panel dataset
> ### Aliases: cat2cat_agg
> 
> ### ** Examples
> 
> data("verticals", package = "cat2cat")
> agg_old <- verticals[verticals$v_date == "2020-04-01", ]
> agg_new <- verticals[verticals$v_date == "2020-05-01", ]
> 
> # cat2cat_agg - can map in both directions at once
> # although usually we want to have the old or the new representation
> 
> agg <- cat2cat_agg(
+   data = list(
+     old = agg_old,
+     new = agg_new,
+     cat_var_old = "vertical",
+     cat_var_new = "vertical",
+     time_var = "v_date",
+     freq_var = "counts"
+   ),
+   Automotive %<% c(Automotive1, Automotive2),
+   c(Kids1, Kids2) %>% c(Kids),
+   Home %>% c(Home, Supermarket)
+ )
> 
> ## possible processing
> library("dplyr")
Error in library("dplyr") : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'sparklyr'

Packages suggested but not available for checking: 'rmarkdown', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) evaluateClusterQuality.Rd:13: Lost braces
    13 | assessors, \code{J} products, code{M} attributes where CATA data have values 
       |                                   ^
checkRd: (-1) homogeneity.Rd:12: Lost braces
    12 | assessors, \code{J} products, code{M} attributes where CATA data have values 
       |                                   ^
checkRd: (-1) inspect.Rd:12: Lost braces
    12 | assessors, \code{J} products, code{M} attributes where CATA data have values 
       |                                   ^
Packages required but not available:
  'dplyr', 'mapSpain', 'sf', 'stringi', 'terra', 'xml2'

Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'slippymath', 'testthat', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rms', 'mlogit', 'Ecdat', 'geepack', 'lme4', 'vcdExtra', 'glmnet',
  'e1071', 'penalized'
Note: skipping ‘loglinear-leukoplakia.Rnw’ due to unavailable dependencies:
  'vcdExtra'
Note: skipping ‘multinomial-travel.Rnw’ due to unavailable dependencies:
  'mlogit', 'Ecdat'
Note: skipping ‘multivariate-knee.Rnw’ due to unavailable dependencies:
  'geepack'
Note: skipping ‘ordinal-knee1.Rnw’ due to unavailable dependencies: 'rms'
Note: skipping ‘random-knee2.Rnw’ due to unavailable dependencies: 'lme4'
Package required but not available: ‘optimx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ruv', 'sva', 'leapp'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DescTools', 'Hmisc', 'broom'

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:
  'ade4', 'ape', 'e1071', 'rasterVis', 'hypervolume', 'FD', 'geometry'

Packages suggested but not available for checking:
  'entropart', 'picante', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'tidyr', 'dplyr', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'viridis', 'lubridate', 'tidyverse', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) catmapdata.Rd:9-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:20-21: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/caTools.Rcheck/00install.out’ for details.
Packages required but not available: 'rms', 'rgenoud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'testthat'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'tidyr', 'openxlsx'

Packages suggested but not available for checking: 'rmarkdown', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'Rcpp', 'RcppParallel', 'RcppArmadillo', 'RcppGSL'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rfast', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phylolm', 'nloptr'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'spelling', 'geiger', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'dplyr', 'ggplot2', 'tidyr', 'igraph', 'stringr',
  'cowplot', 'reticulate'

Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cdcsis', 'sva', 'MatchIt', 'dplyr'

Packages suggested but not available for checking:
  'tidyr', 'rmarkdown', 'testthat', 'covr', 'roxygen2', 'ks', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'bookdown', 'tidyverse', 'ggalt', 'cobalt', 'ggsci',
  'modEvA', 'naniar', 'DT', 'Hmisc', 'hrbrthemes', 'summarytools'
Packages required but not available:
  'SuppDists', 'CBPS', 'PSweight', 'spelling'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcalg', 'igraph', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Packages suggested but not available for checking:
  'BayesTree', 'dplyr', 'Hmisc', 'reshape2', 'rmarkdown', 'testthat',
  'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'SuperLearner', 'xgboost', 'wCorr', 'ggplot2', 'Rcpp', 'Ecume',
  'cowplot'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'ranger', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bsts', 'Boom', 'ggplot2'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'MixMatrix'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'SuperLearner'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geepack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'Rcpp', 'shiny'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CBPS', 'ggplot2', 'lbfgsb3c', 'osqp', 'Rcpp', 'torch', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'reticulate', 'rkeops', 'rmarkdown', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dagitty', 'dplyr', 'ggdag', 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'Rcpp', 'dagitty', 'rstan', 'rstantools', 'stringr',
  'ggdag', 'latex2exp', 'ggplot2', 'RcppArmadillo', 'RcppEigen',
  'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'DeclareDesign', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘causalsens.Rnw’
Engines should be specified as \VignetteEngine{PKG::ENG}.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ranger', 'np', 'hdm', 'SuperLearner', 'glmnet', 'xgboost', 'e1071',
  'fastDummies', 'grf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cowplot', '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: 'Rcpp', 'sitmo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggforce', 'ggrepel', 'ggplot2', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'metap', 'dplyr', 'stringr', 'ggplot2', 'tidyr', 'pheatmap',
  'readr', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'DoE.base', 'fastDummies', 'ggplot2', 'idefix', 'logitr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyr', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'lightgbm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MatchIt', 'glmnet'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'shiny', 'testthat', 'sf'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'dplyr', 'terra', 'stars', 'lwgeom'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcaPP', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'FNN'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hdbinseg’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'diceR', 'tidyr', 'plyr'

Packages suggested but not available for checking: 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RANN', 'Rcpp', 'r2r', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'readr', 'MCMCpack', 'ufs', 'RcppAlgos', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'cds', 'dplyr', 'lsbclust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'testthat', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'igraph'

Packages suggested but not available for checking: 'testthat', 'nnTensor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R2jags', 'rjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'dplyr', 'shiny', 'bs4Dash', 'fresh', 'DT', 'readxl',
  'rmarkdown', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ddpcr', 'RcppArmadillo', 'RcppDist', 'RcppNumerical',
  'RcppEigen'

Packages suggested but not available for checking: 'ggplot2', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'RSQLite', 'rmarkdown'
Packages required but not available:
  'cdmTools', 'GDINA', 'ggplot2', 'cowplot'

Package suggested but not available for checking: ‘CDM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'Rcpp'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'dplyr', 'readr', 'lubridate'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘caret’

Packages suggested but not available for checking: 'gbm', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'dbplyr', 'readr', 'stringr', 'stringi', 'fs', 'tidyr',
  'snakecase'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'duckdb', 'RSQLite', 'RPostgres', 'odbc',
  'ggplot2', 'bigrquery', 'DatabaseConnector', 'lubridate', 'testthat',
  'pool'

Packages which this enhances but not available for checking:
  'arrow', 'CirceR', 'Capr', 'visR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'BIFIEsurvey', 'miceadds'

Packages which this enhances but not available for checking:
  'dina', 'GDINA', 'mirt', 'rrum'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GDINA', 'ggplot2', 'sirt', 'fungible'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette without corresponding tangle output:
  ‘CDNmoney.Stex’
Packages required but not available: 'ggplot2', 'tidyr', 'broom'

Package suggested but not available for checking: ‘eemR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'freqparcoord', 'partools'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'dplyr', 'rjson', '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:
  'geojsonsf', 'lubridate', 'lutz', 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readODS', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘covr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CEC.Rcheck/00install.out’ for details.
Packages required but not available:
  'mixtools', 'ggplot2', 'dplyr', 'ggsci', 'ggridges', 'ggprism'

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rlibeemd', 'forecast', 'LSTS', 'caret', 'e1071'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘anticlust’

Package suggested but not available for checking: ‘nloptr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Package required but not available: ‘RANN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sdcHierarchies', 'digest', 'sdcTable', 'ptable'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘iterpc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'scUtils', 'ggplot2', 'viridis', 'cowplot', 'dplyr', 'scales',
  'scattermore'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'Seurat', 'DESeq2', 'RcppAnnoy',
  'SeuratObject'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'wordspace', 'rmarkdown', 'uwot', 'dendextend',
  'ggplot2', 'ggbeeswarm'
checkRd: (-1) aggregate.tracks.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aggregate.tracks.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repairGaps.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repairGaps.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repairGaps.Rd:20-23: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘gplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'scales', 'ggplot2', 'rrcov', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'robustHD', 'rospca', 'GSE'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MatchIt’

Package suggested but not available for checking: ‘Amelia’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’
Errors in running code in vignettes:
when running code in ‘cencrne.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘cencrne.Rmd’ using ‘UTF-8’... failed to complete the test
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'icenReg', 'condSURV', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'sf', 'stringr', 'memoise', 'tinytiger'

Packages suggested but not available for checking:
  'roxygen2', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MomTrunc', 'ggplot2', 'tlrmvnmvt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘duckdb’

Packages suggested but not available for checking:
  'testthat', 'covr', 'dplyr', 'dbplyr', 'ggplot2', 'chilemapas'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arrow', 'dplyr'

Packages suggested but not available for checking:
  'covr', 'geobr', 'ggplot2', 'rmarkdown', 'scales', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'parsnip', 'dials', 'dplyr', 'prodlim', 'tidyr'

Packages suggested but not available for checking:
  'aorsf', 'covr', 'flexsurv', 'glmnet', 'ipred', 'pec', 'rmarkdown',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maxLik', 'miscTools', 'plm'

Package suggested but not available for checking: ‘AER’

Package which this enhances but not available for checking: ‘sampleSelection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'optimx', 'raster', 'tlrmvnmvt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'ggrepel', 'scales', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) listCensusApis.Rd:10: Lost braces; missing escapes or markup?
    10 | Scrapes {https://api.census.gov/data.json} and returns a dataframe
       |         ^
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking: 'rmarkdown', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘linkcomm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'haven', 'dplyr', 'urltools', 'stringr'

Packages suggested but not available for checking:
  'R.rsp', 'ggplot2', 'tidyr', 'rmarkdown', 'vtable', 'compareGroups'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gravity’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
Packages required but not available:
  'terra', 'dplyr', 'fs', 'slippymath', 'vapour', 'stringr', 'wk'

Packages suggested but not available for checking:
  'covr', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'CBPS', 'twang', 'Rcpp', 'glmnet', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rrcov’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘igraph’

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: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xml2', 'batchtools', 'reshape'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'batchtools', 'dplyr', 'DT', 'ggplot2', 'htmltools', 'plotly',
  'reshape', 'shiny', 'shinyjs', 'shinyWidgets', 'shinymaterial',
  'shinyjqui', 'sortable', 'xml2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'haven', 'readr', 'labelled', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'DALEX'

Packages suggested but not available for checking:
  'ggiraph', 'e1071', '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: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'janitor', 'progressr', 'Rcpp', 'RcppParallel', 'stringr',
  'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'ggrepel', 'qs', 'rmarkdown', 'RSQLite', 'stringi',
  'testthat', 'usethis', 'xgboost'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘jsonvalidate’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'dagitty', 'igraph', 'mockery', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'scales', 'ggplot2', 'testthat', 'bookdown',
  'spelling', 'distributional'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > # nolint start
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'plyr', 'dplyr', 'osmdata', 'tidync', 'future', 'furrr', 'sf',
  'tidyr'

Packages suggested but not available for checking: 'lubridate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'osqp', 'cgam', 'gratia', 'coneproj', 'TruncatedNormal'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'coneproj', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'ggplot2', 'reshape2', 'plyr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'readxl', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyverse', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BayesFactor', 'DescTools', 'dplyr', 'ggmosaic', 'ggplot2',
  'ggrepel', 'paletteer', 'scales', 'sjstats', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'BSDA', 'ggthemes', 'hrbrthemes', 'janitor', 'productplots',
  'rmarkdown', 'stringi', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Hmisc', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gmp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'systemfit', 'cplm', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'umap'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'vdiffr'
checkRd: (-1) ftse100.Rd:8: Lost braces; missing escapes or markup?
     8 |  This dataset gives the daily returns (c_{t+1}/c_t -1) of the UK FTSE 100 index from 2nd April 1984 until the 13th September 2012.
       |                                          ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'glmnet', 'ks', 'data.tree', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'DiagrammeR', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'dplyr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in Rd file 'multiplierDSeqfun.Rd':
  ‘MC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available:
  'phylobase', 'raster', 'dplyr', 'rangeModelMetadata', 'sf'

Packages suggested but not available for checking:
  'ape', 'tidyverse', 'rmarkdown', 'testthat', 'picante', 'wallace',
  'dismo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'available', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ChannelAttribution', 'shiny', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘AER’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'lax', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rgl', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ipaddress', 'stringi'
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'future', 'igraph', 'pdftools', 'xml2', '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: 'miniUI', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fs’

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'spelling', 'testthat'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘htmltools’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘quarto’
checkRd: (-1) as.data.frame.checkglobals.Rd:43: Lost braces; missing escapes or markup?
    43 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
checkRd: (-1) as.matrix.checkglobals.Rd:32: Lost braces; missing escapes or markup?
    32 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
Packages required but not available:
  'devtools', 'dplyr', 'rcmdcheck', 'roxygen2', 'stringr'

Packages suggested but not available for checking:
  'attachment', 'rmarkdown', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'ggplot2', 'rmarkdown', 'testthat'
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'darts'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'lubridate', 'rmarkdown', 'testthat', 'tidyr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cheddar.Rcheck/00install.out’ for details.
Packages required but not available:
  'spinifex', 'ggplot2', 'plotly', 'shiny', 'shinythemes',
  'shinycssloaders', 'DT', 'conflicted'

Packages suggested but not available for checking:
  'tourr', 'gganimate', 'dplyr', 'tidyr', 'beepr', 'testthat',
  'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'kableExtra', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'ggplot2', 'reshape2', 'phyloseq'

Packages suggested but not available for checking:
  'patchwork', 'ggpmisc', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MSQC', 'e1071', 'pROC', 'caret'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'webchem', 'fmcsR', 'ChemmineR', 'hillR', 'ape', 'GUniFrac',
  'tidygraph', 'igraph', 'ggraph', 'ggplot2', 'ggdendro', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'e1071', 'pcaPP', 'som'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ChemoSpecUtils', 'readJDX', 'ggplot2'

Packages suggested but not available for checking:
  'mlrMBO', 'smoof', 'mlr', 'lhs', 'RcppRoll', 'rmarkdown', 'bookdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ChemoSpecUtils', 'reshape2', 'readJDX', 'patchwork', 'ggplot2',
  'plotly'

Packages suggested but not available for checking:
  'js', 'pcaPP', 'speaq', 'rmarkdown', 'bookdown', 'chemometrics',
  'hyperSpec', 'amap', 'roxut'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'plotly'

Packages suggested but not available for checking:
  'ChemoSpec', 'ChemoSpec2D', 'amap', 'roxut', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'testthat'
Running examples in ‘cherryblossom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run09
> ### Title: Cherry Blossom Run data, 2009
> ### Aliases: run09
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘hommel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'sf', 'tidyr'

Packages suggested but not available for checking:
  'igraph', 'patchwork', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom', 'ggplot2', 'dplyr'

Packages suggested but not available for checking: 'spelling', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'dunlin', 'formatters', 'ggplot2', 'nestcolor', 'rlistings',
  'rtables', 'stringr', 'tern'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'tidyr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bedr', 'rmarkdown'

Packages suggested but not available for checking:
  'testthat', 'GenomicInteractions', 'Gviz', 'countreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'dbplyr', 'dplyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'reshape2', 'purrrlyr'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'rmapshaper', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'chillR', 'dplyr', 'lubridate', 'ggplot2'
Packages required but not available:
  'dplyr', 'ecmwfr', 'fields', 'GenSA', 'ggplot2', 'lubridate', 'metR',
  'patchwork', 'plyr', 'raster', 'Rcpp', 'readxl', 'reshape2',
  'scales', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'jiebaR', 'tm', 'stringi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bruceR’

Packages suggested but not available for checking: 'car', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ptw', 'shiny'

Packages suggested but not available for checking:
  'drc', 'qpcR', 'RDML', 'rmarkdown', 'spelling', 'testthat'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ChIPtest.Rcheck/00install.out’ for details.
Packages required but not available: 'sf', 'terra'

Packages suggested but not available for checking:
  'climatrends', 'rmarkdown', 'testthat', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘gt’

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:
  'cmdstanr', 'rmarkdown', 'posterior'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'
Running examples in ‘chk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: expect_chk_error
> ### Title: Expect Chk Error
> ### Aliases: expect_chk_error
> 
> ### ** Examples
> 
> expect_chk_error(chk_true(FALSE))
Error in expect_chk_error(chk_true(FALSE)) : `testhat` must be installed.
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'tufte'
checkRd: (-1) logB.to.OBIGT.Rd:39: Lost braces
    39 | To avoid overfitting, only the first three parameters (code{G}, \code{S}, and \code{c1}) are used by default.
       |                                                            ^
checkRd: (-1) util.fasta.Rd:39: Lost braces; missing escapes or markup?
    39 | If {id} is not given, and a UniProt FASTA header is detected (regular expression \code{"\\|......\\|.*_"}), information there (accession, name, organism) is split into the \code{protein}, \code{abbrv}, and {organism} columns of the resulting data frame.
       |    ^
checkRd: (-1) util.fasta.Rd:39: Lost braces; missing escapes or markup?
    39 | If {id} is not given, and a UniProt FASTA header is detected (regular expression \code{"\\|......\\|.*_"}), information there (accession, name, organism) is split into the \code{protein}, \code{abbrv}, and {organism} columns of the resulting data frame.
       |                                                                                                                                                                                                               ^
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'bayesm', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'stringr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'elevatr', 'geosphere', 'ggplot2', 'igraph', 'tanaka', 'terra',
  'threejs'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Packages required but not available:
  'acs', 'Hmisc', 'stringr', 'ggplot2', 'dplyr', 'ggmap', 'tigris',
  'xml2', 'rvest', 'tidyr', 'tidycensus'

Packages suggested but not available for checking:
  'testthat', 'choroplethrAdmin1', 'rmarkdown', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'Ryacas'

Package suggested but not available for checking: ‘scales’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘animation’

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', 'readxl', 'reticulate', 'stringr', 'tidyr', 'xml2'

Packages suggested but not available for checking:
  'entab', 'mzR', '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: 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmltools', 'htmlwidgets'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fastmap', 'later', 'promises', 'websocket'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'dplyr', 'dygraphs', 'ggplot2', 'plotly', 'prettydoc', 'readr',
  'rmarkdown', 'rmdformats', 'scales', 'skimr', 'viridis'

Packages suggested but not available for checking:
  'bookdown', 'devtools', 'flexdashboard', 'pagedown', 'rolldown',
  'rticles', 'tufte', 'xaringan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'lubridate', 'rmarkdown', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'magick', 'readr', 'tidyr'

Packages suggested but not available for checking:
  'readxl', 'testthat', 'rmarkdown', 'covr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'scales', 'ggplot2'
Packages required but not available: 'dplyr', 'LaF'

Packages suggested but not available for checking:
  'testthat', 'RSQLite', 'dbplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spelling', 'testthat', 'rmarkdown'
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggraph'

Packages suggested but not available for checking:
  'clustree', 'ComplexHeatmap', 'plotly', 'Seurat', 'testthat',
  'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lamW’

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:
  'RNifti', 'plotly', 'neurobase', 'oro.nifti', 'servr', 'htmltools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'ggplot2', 'doRNG', 'rngtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘kableExtra’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xml2', 'oro.nifti', 'gifti'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'gifti', 'oro.nifti', 'RNifti', 'rgl', 'xml2'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'ggpubr', 'htmlwidgets', 'manipulateWidget',
  'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'dplyr', 'tidyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BART', 'twang', 'arm', 'dplyr', 'Matching', 'WeightIt', 'tmle',
  'tidyr', 'ggplot2', 'cowplot', 'metR', 'stringr', 'SuperLearner'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ChIPseeker', 'DESeq2', 'dplyr', 'edgeR', 'fgsea',
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene', 'ggplot2', 'ggrepel',
  'pheatmap', 'sva'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tm', 'tidytext', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'igraph', 'centiserve', 'FactoMineR', 'factoextra', 'GGally',
  'pheatmap', 'dendextend', 'viridis', 'ggplot2', 'Rtsne', 'plyr',
  'intergraph'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'BSDA', 'userfriendlyscience'
checkRd: (-1) CIplot.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat', 'usethis', 'vcr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'testthat', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dendextend', 'ComplexHeatmap', 'covr', 'rmarkdown'
Running examples in ‘circlize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: circos.dendrogram
> ### Title: Add circular dendrograms
> ### Aliases: circos.dendrogram
> 
> ### ** Examples
> 
> load(system.file(package = "circlize", "extdata", "bird.orders.RData"))
> 
> labels = hc$labels  # name of birds
> ct = cutree(hc, 6)  # cut tree into 6 pieces
> n = length(labels)  # number of bird species
> dend = as.dendrogram(hc)
> 
> circos.par(cell.padding = c(0, 0, 0, 0))
> circos.initialize(sectors = "a", xlim = c(0, n)) # only one sector
> max_height = attr(dend, "height")  # maximum height of the trees
> circos.trackPlotRegion(ylim = c(0, 1), bg.border = NA, track.height = 0.3,
+     panel.fun = function(x, y) {
+         for(i in seq_len(n)) {
+             circos.text(i-0.5, 0, labels[i], adj = c(0, 0.5),
+                 facing = "clockwise", niceFacing = TRUE,
+                 col = ct[labels[i]], cex = 0.7)
+         }
+ })
> 
> suppressPackageStartupMessages(require(dendextend))
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘dendextend’
> dend = color_branches(dend, k = 6, col = 1:6)
Error in color_branches(dend, k = 6, col = 1:6) : 
  could not find function "color_branches"
Execution halted
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘circlize.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
Package required but not available: ‘energy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'RInside', 'ggplot2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |     ^
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |            ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NPCirc', 'ggplot2'

Packages suggested but not available for checking:
  'plotly', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'OptCirClust', 'Rcpp'

Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'htmlTable', 'Rcpp', 'scales',
  'tidyr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'ggrepel', 'kableExtra', 'rmarkdown', 'roxygen2', 'testthat',
  'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) doseFind.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'agop', 'RSQLite', 'stringi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'MESS', 'networkD3', 'scales'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘crul’

Packages suggested but not available for checking:
  'testthat', 'vcr', 'webmockr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'tidyr', 'ggthemes'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'dplyr', 'lme4'

Packages suggested but not available for checking: 'ggplot2', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'plotly', 'ggraph', 'igraph', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cit.Rcheck/00install.out’ for details.
Packages required but not available:
  'ggplot2', 'GGally', 'clustMixType', 'stringr', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ggplot2'

Packages suggested but not available for checking: 'caret', 'gbm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future', 'memoise'

Packages suggested but not available for checking:
  'feather', 'ggplot2', 'rmarkdown', 'roxygen2', 'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'kcmeans'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘optimx’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'lubridate', 'stringr', 'memoise'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BART', 'tidyr', 'ggplot2', 'randomForestSRC'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'fields', 'gplots'

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', 'survey', 'DT', 'shiny', 'shinyjs'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'crul', 'dplyr', 'dbplyr'

Packages suggested but not available for checking:
  'sf', 'readxl', 'testthat', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CompQuadForm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggforce', 'ggplot2', 'ggraph', 'igraph', 'Rcpp', 'readr',
  'stringr', 'tidygraph', 'tidyr', 'vroom'

Packages suggested but not available for checking: 'rmarkdown', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phytools', 'strap'

Packages suggested but not available for checking: 'rgl', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgl', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘FRAPO’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
checkRd: (-1) get_langs.Rd:13: Lost braces
    13 | character vector listing all the languages that tag API call supports. See \code{\link{tag_images}} and code{\link{tag_image_urls}}
       |                                                                                                             ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'marginaleffects', 'mvnfast'

Packages suggested but not available for checking:
  'testthat', 'MatchIt', 'rmarkdown', 'Amelia', 'survey', 'estimatr',
  'fixest', 'logistf', 'geepack', 'rms', 'robust', 'AER', 'ivreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cd01-0-distanceMatrix.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd01-0-distanceMatrix.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cd02-1-cluster3.Rd:25: Lost braces
    25 |   Kevin R. Coombes email{krc@silicovore.com}
       |                         ^
checkRd: (-1) cd03-0-ClusterTest-class.Rd:70: Lost braces
    70 |   Kevin R. Coombes email{krc@silicovore.com}
       |                         ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'Rcpp', 'ROCR', 'caret'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘e1071’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘e1071’

Packages suggested but not available for checking: 'units', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'e1071', 'cellWise', 'kernlab'

Packages suggested but not available for checking:
  'reshape2', 'robCompositions'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'testthat', 'readtext', 'cld3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'testthat', 'cld2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'testthat'
checkRd: (-1) clean.Rd:136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:142: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # ==================================================================== #
  > # TITLE                                                                #
  > # cleaner: Fast and Easy Data Cleaning                                 #
  > #                                                                      #
  > # SOURCE                                                               #
  > # https://github.com/msberends/cleaner                                 #
  > #                                                                      #
  > # LICENCE                                                              #
  > # (c) 2022 Berends MS (m.s.berends@umcg.nl)                            #
  > #                                                                      #
  > # This R package is free software; you can freely use and distribute   #
  > # it for both personal and commercial purposes under the terms of the  #
  > # GNU General Public License version 2.0 (GNU GPL-2), as published by  #
  > # the Free Software Foundation.                                        #
  > #                                                                      #
  > # This R package was publicly released in the hope that it will be     #
  > # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
  > # ==================================================================== #
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘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: 'udpipe', 'reticulate', 'stringi'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'htmltools', 'rmarkdown'

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', 'rasciidoc', 'rmarkdown', 'testthat', 'usethis'

VignetteBuilder package required for checking but not installed: ‘rasciidoc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gganimate', 'ggplot2', 'ggtext', 'transformr', 'imputeTestbench',
  'imputeTS', 'lubridate', 'shiny', 'stringr'

Packages suggested but not available for checking:
  'rmarkdown', 'timetk', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lintr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'sf', 'raster', 'reshape2', 'plyr', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'selectr', 'xml2'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MCMCpack’

Package suggested but not available for checking: ‘seqHMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘arrow’

Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'stringi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future', 'future.apply'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'reshape2', 'plyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'rvest', 'stringi', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'disordR', 'partitions'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'lubridate', 'xml2', 'ggplot2', 'scales', 'reshape2', 'rvest',
  'stringr'

Packages suggested but not available for checking:
  'spelling', 'rmarkdown', 'pander', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CNLTreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'readr', 'tidyr'

Packages suggested but not available for checking:
  'gganimate', 'lubridate', 'rmarkdown', 'scales', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Packages suggested but not available for checking:
  'rangeBuilder', 'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'fields', 'gstat', 'raster', 'readxl'
Running examples in ‘climatol-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MHisopleths
> ### Title: Isopleths on a months-hours diagram
> ### Aliases: MHisopleths
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(climatol_data)
> MHisopleths(AWS_1year,'Temp',title='Mean temperature (C) -- My airport, 2002')
Error in MHisopleths(AWS_1year, "Temp", title = "Mean temperature (C) -- My airport, 2002") : 
  This function requires the package fields.
Please, install it and re-run the function
Execution halted
Package required but not available: ‘nasapower’

Packages suggested but not available for checking:
  'ag5Tools', 'chirps', 'rmarkdown', 'sf', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geosphere', 'ggplot2', 'reshape2'

Package suggested but not available for checking: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'qpdf'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'climaemet', 'dismo', 'dplyr', 'elevatr', 'exactextractr', 'geodata',
  'plyr', 'sf', 'Ternary', 'terra'

Packages suggested but not available for checking:
  'covr', 'fs', 'raster', 'rmarkdown', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rts', 'raster', 'terra', 'yaImpute'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘extRemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SPEI’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSpectra’

Packages suggested but not available for checking:
  'climatrends', 'gosset', 'nasapower', 'rmarkdown', 'sf',
  'PlackettLuce', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘multiApply’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lubridate', 'lme4', 'reshape', 'RcppRoll'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bookdown', 'clinUtils', 'crosstalk', 'ggplot2', 'haven',
  'htmltools', 'htmlwidgets', 'jsonvalidate', 'plotly', 'plyr',
  'rmarkdown', 'stringr', 'xml2'

Packages suggested but not available for checking:
  'inTextSummaryTable', 'patientProfilesVis', 'testthat', 'DT',
  'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'shiny', 'DoseFinding', 'ggplot2', 'tidyr', 'dplyr',
  'waiter'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'BayesFactor', 'dplyr', 'ggplot2', 'lme4', 'tidyr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'tidyverse', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'ggplot2', 'cowplot', 'nloptr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
Package required but not available: ‘reticulate’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xml2', 'lme4', 'ggplot2', 'pROC', 'stringi', 'scales', 'dplyr',
  'pander'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'crosstalk', 'DT', 'haven', 'htmlwidgets', 'plyr'

Packages suggested but not available for checking:
  'ggplot2', 'plotly', 'htmltools', 'pander', 'rmarkdown', 'testthat',
  'flextable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'qgraph', 'lessR', 'ohenery'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'digest', 'htmltools', 'htmlwidgets', 'mockery', 'rmarkdown',
  'testthat'
Running examples in ‘cli-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: test_that_cli
> ### Title: Test cli output with testthat
> ### Aliases: test_that_cli
> 
> ### ** Examples
> 
> # testthat cannot record or compare snapshots when you run these
> # examples interactively, so you might want to copy them into a test
> # file
> 
> # Default configurations
> cli::test_that_cli("success", {
+   testthat::local_edition(3)
+   testthat::expect_snapshot({
+     cli::cli_alert_success("wow")
+   })
+ })
Error in loadNamespace(x) : there is no package called ‘testthat’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'shiny', 'lme4', 'stringr', 'openxlsx'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'StMoMo', 'ChainLadder', 'ggplot2', 'forecast', 'reshape2'

Packages suggested but not available for checking:
  'rmarkdown', 'apc', 'dplyr', 'tidyr'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'anytime', 'dplyr', 'janitor', 'lubridate', 'stringi', '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: ‘tzdb’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'slider', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'Rcpp', 'Rmpfr', 'rstan', 'rstantools', 'RcppEigen',
  'RcppParallel', 'StanHeaders'

Packages suggested but not available for checking:
  'car', 'covr', 'ggplot2', 'ggsurvfit', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mc2d’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggrepel', 'dbscan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'aws.s3', 'googledrive', 'dplyr'

Packages suggested but not available for checking:
  'googlesheets4', 'haven', 'readr', 'readxl', 'rmarkdown', 'testthat',
  'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tfruns’

Packages suggested but not available for checking:
  'tensorflow', 'keras', 'testthat'

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:
  'httptest', 'kableExtra', 'lintr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rio’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Objects in \usage without \alias in Rd file 'clpm-internal.Rd':
  ‘lpm.newton2’ ‘lpm.fit’ ‘lpm.newton’ ‘L_lambda’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages required but not available: 'popdemo', 'car', 'dplyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'dplyr'

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: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'geepack', 'mlmRev', 'AER', 'plm', 'lme4', 'testthat', 'rmarkdown',
  'covr', 'ivreg'
checkRd: (-1) impute_covariance_matrix.Rd:74-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_covariance_matrix.Rd:80-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_covariance_matrix.Rd:88-98: Lost braces in \itemize; meant \describe ?
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘e1071’

Packages which this enhances but not available for checking:
  'ape', 'kernlab'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘e1071’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'crul', 'devtools', 'ggplot2', 'lintr', 'patchwork', 'prettydoc',
  'rgl', 'rmarkdown', 'roxygen2', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2020-2023 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(clugenr)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Note: skipping ‘examples2d.Rmd’ due to unavailable dependencies:
  'ggplot2', 'patchwork'
Note: skipping ‘examples3d1.Rmd’ due to unavailable dependencies: 'rgl'
Note: skipping ‘examples3d2.Rmd’ due to unavailable dependencies: 'rgl'
Note: skipping ‘examplesmrg.Rmd’ due to unavailable dependencies:
  'ggplot2', 'patchwork'
Note: skipping ‘examplesnd.Rmd’ due to unavailable dependencies:
  'ggplot2', 'patchwork'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'dplyr', 'amap', 'tableone'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fpc', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rgl', 'ggplot2', 'ggpubr', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'scales', 'reshape2', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'Rcpp', 'aricode', 'dplyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'fastcluster', 'igraph', 'Rcpp', 'reshape2',
  'stringr', 'uwot'

Packages suggested but not available for checking:
  'rmarkdown', 'e1071', 'dbscan', 'dendextend', 'Seurat', 'readr',
  'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘FactoMineR’

Package suggested but not available for checking: ‘ClustVarLV’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'IsoGene', 'DoseFinding', 'pheatmap', 'shiny', 'readr', 'DT'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qrcm', 'fda', 'ggpubr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘apcluster’

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cubature', 'lme4'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Found the following files/directories:
  ‘clusterhap_reports’
Packages required but not available:
  'Rcpp', 'Ckmeans.1d.dp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'amap', 'apcluster', 'ClusterR', 'dplyr', 'future', 'ggplot2', 'gmp',
  'shiny', 'sqldf', 'toOrdinal'

Packages suggested but not available for checking:
  'DT', 'shinyalert', 'shinyFiles', 'shinyjs', 'shinythemes',
  'shinyWidgets', 'tidyverse', 'shinycssloaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/clustering.sc.dp.Rcheck/00install.out’ for details.
Packages required but not available:
  'dplyr', 'GSEABase', 'GSVA', 'singscore', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'narray', 'Rcpp'

Packages suggested but not available for checking:
  'BiocParallel', 'devtools', 'rmarkdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'gplots', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'data.tree', 'dendextend', 'reshape', 'reshape2', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘fpc’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'gmp', 'ggplot2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'OpenImageR', 'FD', 'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'plm', 'mlogit', 'dfidx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'e1071'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'copula', 'WeightedCluster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spdep’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ClusterR', 'copula', 'dplyr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking:
  'ggExtra', 'rmarkdown', 'testthat', 'Hmisc', 'spelling', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'reshape2', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BiDAG', 'pcalg', 'RBGL', 'igraph'

Packages suggested but not available for checking:
  'rmarkdown', 'ggraph', 'ggpubr', 'ggplot2', 'reshape2', 'car', 'ks',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BAMBI', 'igraph', 'ggplot2', 'cowplot'

Packages suggested but not available for checking: 'rmarkdown', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'haven', 'rmarkdown'
Packages required but not available:
  'ggplot2', 'rARPACK', 'GGally', 'fpc', 'dplyr', 'plyr', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggraph', 'igraph', 'dplyr', 'ggplot2', 'viridis', 'tidygraph',
  'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'Seurat', 'covr', 'pkgdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringi', 'stringr', 'igraph', 'tidygraph', 'ggraph',
  'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'klaR', 'dplyr', 'psycho'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'plyr', 'RcppEigen'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BMA’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'Rmixmod', 'VarSelLCM', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'annotate', 'GO.db', 'moe430a.db', 'kohonen'
Note: skipping ‘clValid.Rnw’ due to unavailable dependencies:
  'kohonen', 'annotate'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'lubridate', 'optimx', 'Rcpp', 'RcppArmadillo', 'RcppGSL',
  'testthat'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'xml2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'smoof', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) CMAPSS.Rd:10: Lost braces
    10 | \item \code{train}{ a list of class "hhsmm.data" as the train dataset}
       |                   ^
checkRd: (-1) CMAPSS.Rd:11: Lost braces
    11 | \item \code{test}{ a list of class "hhsmm.data" as the test dataset}
       |                  ^
checkRd: (-1) CMAPSS.Rd:12: Lost braces
    12 | \item \code{subsets}{ a matrix containig the number of units in each subset of the CMAPSS data set (FD001-FD004) for the train and test datasets}
       |                     ^
Packages required but not available:
  'readxl', 'ggplot2', 'dplyr', 'scales', 'reshape2', 'stringr'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'Ryacas0', 'ROCR'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) cmb.search.Rd:50: Lost braces; missing escapes or markup?
    50 |   \item{order}{applied conditioning order {length p}}
       |                                           ^
checkRd: (-1) gp.realize.Rd:20: Lost braces; missing escapes or markup?
    20 | The list \code{l.v} is created by \code{makedistlist()} from a {n x p} design matrix on which to generate the unconditional GP realization.  The correlation parameters take on values in \code{(0,1)} and use the Gaussian correlation model, calculated as \code{rho^d(xi,xj)^2}.  This helper function is used to create the demonstration data used in the example for \code{calibrate()}.
       |                                                                ^
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'x3ptools', 'dplyr', 'ggplot2', 'imager', 'stringr', 'scales',
  'ggnewscale', 'tidyr', 'patchwork', 'ggplotify'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'DT', 'magick', 'rgl', 'covr', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'testthat', 'usethis'

Packages suggested but not available for checking: 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'glmnet', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CMF.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'MatrixExtra', 'recosystem', 'recommenderlab', 'rmarkdown',
  'kableExtra'
Running examples in ‘cmfrec-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CMF.from.model.matrices
> ### Title: Create a CMF model object from fitted matrices
> ### Aliases: CMF.from.model.matrices
> 
> ### ** Examples
> 
> ### Example 'adopting' a model from 'recosystem'
> library(cmfrec)
> library(recosystem)
Error in library(recosystem) : there is no package called ‘recosystem’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'digest', 'readr', 'stringr', 'aws.s3'

Packages suggested but not available for checking:
  'scales', 'cancensus', 'ggplot2', 'tidyr', 'rmarkdown', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RJSONIO’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fastDummies', 'survey', 'robCompositions', 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'devtools', 'roxygen2'
checkRd: (-1) bvp.Rd:24: Lost braces
    24 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivp.Rd:38: Lost braces
    38 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivpsys.Rd:29: Lost braces
    29 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
Running ‘testthat.R’ [0s/1s]
Running 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: 'rmarkdown', 'ggplot2'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'twang'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'tidyverse', 'ggpubr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fields', 'FNN', 'raster', 'trend'

Packages suggested but not available for checking:
  'cmsaf', 'cmsafvis', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cmsafops', 'cmsafvis', 'colourpicker', 'FNN', 'raster', 'shiny',
  'shinyFiles', 'shinyjs', 'shinythemes', 'shinyWidgets', 'xml2'

Packages suggested but not available for checking: 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cmsafops', 'fields', 'raster', 'sf', 'terra', 'rasterVis'

Packages suggested but not available for checking:
  'animation', 'FNN', 'rnaturalearth', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'shinyMatrix', 'caret', 'e1071'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'rvest', 'xml2'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'kSamples'

Packages suggested but not available for checking:
  'lintr', 'rmarkdown', 'spelling', 'testthat', 'tidyr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'censReg', 'AER', 'rmarkdown', 'maxLik', 'bookdown', 'tobit1'
Running examples in ‘cmtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cmtest
> ### Title: Conditional moments test
> ### Aliases: cmtest cmtest.tobit cmtest.tobit1 cmtest.censReg cmtest.glm
> ### Keywords: htest
> 
> ### ** Examples
> 
> # replication of Wells (2003) and Pagan and Vella (1989) using Fair's data
> library("AER")
Error in library("AER") : there is no package called ‘AER’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'plyr', 'dplyr', 'r2d3', 'ggplot2', 'stringr'

Packages suggested but not available for checking:
  'htmltools', 'readxl', 'testthat', 'rmarkdown', 'widgetframe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cna', 'Rcpp', 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'car'

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', 'rmarkdown'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rgl', 'shapes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘miscTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CNLTreg', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘latticeExtra’

Packages suggested but not available for checking:
  'shiny', 'shinycssloaders', 'readxl', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘e1071’
Packages required but not available: 'stringr', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'RcppParallel',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tidyr', 'reshape2', 'jointseg', 'shiny',
  'GenomicInteractions', 'OpenImageR', 'biomaRt', 'plyr', 'dplyr',
  'stringr', 'rtracklayer', 'Hmisc'

Packages suggested but not available for checking:
  'ComplexHeatmap', 'rmarkdown', 'igraph', 'visNetwork', 'plotly',
  'InteractionSet', 'GenomicFeatures', 'shinythemes',
  'shinycssloaders', 'DT', 'heatmaply', 'shinyjs', 'htmltools',
  'htmlwidgets', 'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'digest', 'Rcpp', 'scrm', 'RcppArmadillo'

Packages suggested but not available for checking:
  'PopGenome', 'phyclust', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rvest', 'xml2', 'lubridate', 'stringr', 'tidyr', 'dplyr', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'tidyr', 'fields', 'readxl', 'ggplot2', 'sfheaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggparty', 'ggtext'

Packages suggested but not available for checking: 'disttree', 'MethComp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'MatchIt', 'WeightIt', 'twang', 'twangContinuous', 'Matching',
  'optmatch', 'CBPS', 'designmatch', 'optweight', 'mice', 'MatchThem',
  'cem', 'sbw', 'gbm', 'caret', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in Rd file 'lb_calculation.Rd':
  ‘qu.param’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'fpc', 'glmnet', 'pheatmap'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'dplyr', 'tidyr', 'ggplot2', 'ggtern', 'DT'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'forecast', 'ggplot2', 'StanHeaders', 'RcppParallel'

Packages suggested but not available for checking: 'covr', 'testthat'

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: ‘rkward’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in testthat/tests.r
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Documented arguments not in \usage in Rd file 'cocorresp-internal.Rd':
  ‘Y’ ‘eps’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ## Test `analogue` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’

Package which this enhances but not available for checking: ‘rkward’
Running ‘test.cocron.package.R’ [0s/1s]
Running the tests in ‘tests/test.cocron.package.R’ failed.
Complete output:
  > # the tests are realized using the "testthat" package
  > # and can be found in ../inst/tests
  > 
  > require(testthat)
  Loading required package: testthat
  Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'testthat'
  > test_package("cocron")
  Error in test_package("cocron") : could not find function "test_package"
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'plyr', 'pROC', 'ggpubr', 'ggplot2', 'ComplexHeatmap',
  'survminer'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tensorflow', 'keras', 'pROC'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future', 'future.apply'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'compositions', 'ggplot2', '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:
  'rmdpartials', 'ggplot2', 'stringr', 'dplyr', 'tidyr', 'haven',
  'likert', 'skimr', 'htmltools', 'labelled'

Packages suggested but not available for checking:
  'testthat', 'DT', 'shinytest', 'lme4', 'rmarkdown', 'shiny',
  'miniUI', 'roxygen2', 'rio', 'future', 'ufs', 'userfriendlyscience'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'haven', 'flextable', 'dplyr', 'officer', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘beepr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Epi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages suggested but not available for checking:
  'highlight', 'RJSONIO', 'Rcpp'
checkRd: (-1) asVarName.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) asVarName.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) asVarName.Rd:28-30: Lost braces in \itemize; meant \describe ?
Running examples in ‘CodeDepends-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: highlightCode
> ### Title: Display R code with highlighting of variables, links to
> ###   functions and packages
> ### Aliases: highlightCode
> ### Keywords: programming
> 
> ### ** Examples
> 
> f = system.file("samples", "sitepairs.R", package = "CodeDepends")
> ## url checking takes a while, too long for CRAN example
> highlightCode(f, "foo.html", checkURLs=FALSE)
Loading required namespace: highlight
Failed with error:  ‘there is no package called ‘highlight’’
Error in highlightCode(f, "foo.html", checkURLs = FALSE) : 
  Unable to highlight code without the highlight and/or RJSONIO package(s)
Execution halted
Packages required but not available:
  'CDMConnector', 'duckdb', 'dplyr', 'stringr', 'tidyr', 'lubridate',
  'PatientProfiles', 'RJSONIO'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat', 'RPostgres', 'odbc', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'crul', 'memoise', 'urltools', 'xml2'

Packages suggested but not available for checking:
  'covr', 'details', 'dplyr', 'jsonld', 'jsonvalidate', 'rmarkdown',
  'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'bvpSolve', 'testthat'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggplot2', 'readr', 'imputeTS', 'scales', 'tensorflow', 'keras',
  'narray', 'fastDummies', 'philentropy', 'greybox', 'lubridate'

Packages suggested but not available for checking: 'testthat', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'kableExtra', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'readr', 'REDCapR', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'plyr', 'visNetwork', 'reshape2'

Packages suggested but not available for checking: 'rmarkdown', 'wTO'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fractional’

Packages suggested but not available for checking:
  'dplyr', 'car', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'reshape2', 'devtools', 'dplyr', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running 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: ‘openxlsx’

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'plyr', 'reshape2', 'useful', 'dplyr', 'dygraphs',
  'plotly'

Packages suggested but not available for checking:
  'testthat', 'covr', 'glmnet', 'maxLik', 'xgboost', 'workflows',
  'parsnip', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ## Test `coenocliner` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

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: ‘rmarkdown’
Packages required but not available: 'gplots', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'cubature', 'RcppGSL'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyjs', 'dplyr', 'paws'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) kprime.Rd:36: Lost braces; missing escapes or markup?
    36 | kprime is a {p,d,q} set of functions that compute the K-prime distribution. This distribution has many applications,
       |             ^
checkRd: (-1) lsecond.Rd:37: Lost braces; missing escapes or markup?
    37 | lsecond are {p,d,q} functions that compute the Lambda-second (L") distribution. This
       |             ^
checkRd: (-1) pilsecond.Rd:39: Lost braces; missing escapes or markup?
    39 | pilsecond are {p,d,q} functions that compute the prior-informed Lambda-second (L") distribution. This
       |               ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DatabaseConnector', 'dplyr'

Packages suggested but not available for checking:
  'Andromeda', 'rmarkdown', 'testthat'

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:
  'testthat', 'shiny', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DatabaseConnector', 'dplyr', 'ParallelLogger'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'plotly', 'tidyr', 'openxlsx'

Packages suggested but not available for checking: 'rmarkdown', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'dtplyr', '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:
  'CDMConnector', 'dplyr', 'dbplyr', 'lubridate', 'broom',
  'PatientProfiles', 'scales', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'CodelistGenerator', 'roxygen2', 'rmarkdown', 'ggplot2',
  'duckdb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Epi', 'ggplot2', 'DiagrammeR', 'DiagrammeRsvg'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'aphid', 'seqinr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘e1071’
Errors in running code in vignettes:
when running code in ‘Implementation.Rnw’
  ...

> options(prompt = "R> ", continue = "+  ")

> library("coin")
Loading required package: survival

> library("e1071")

  When sourcing ‘Implementation.R’:
Error: there is no package called ‘e1071’
Execution halted

  ‘Implementation.Rnw’ using ‘UTF-8’... failed
  ‘LegoCondInf.Rnw’ using ‘UTF-8’... [6s/6s] OK
  ‘MAXtest.Rnw’ using ‘UTF-8’... [21s/23s] OK
  ‘coin.Rnw’ using ‘UTF-8’... [4s/4s] OK
Note: skipping ‘Implementation.Rnw’ due to unavailable dependencies:
  'e1071'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'openxlsx', 'ggplot2', 'readxl'

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat', 'Compind', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nlsr’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'fastverse', 'plm', 'fixest', 'RcppArmadillo', 'RcppEigen', 'dplyr',
  'ggplot2', 'scales', 'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'data.tree'

Packages suggested but not available for checking: 'dplyr', 'testthat'

Package which this enhances but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'furrr', 'ggplot2', 'rmarkdown', 'testthat'
Running examples in ‘collateral-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: collateral_mappers
> ### Title: Map over a list while capturing side effects.
> ### Aliases: collateral_mappers map_safely map_quietly map_peacefully
> ###   map2_safely map2_quietly map2_peacefully pmap_safely pmap_quietly
> ###   pmap_peacefully future_map_safely future_map_quietly
> ###   future_map_peacefully future_map2_safely future_map2_quietly
> ###   future_map2_peacefully future_pmap_safely future_pmap_quietly
> ###   future_pmap_peacefully
> 
> ### ** Examples
> 
> 
> library(tibble)
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘gmp’

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'devtools', 'covr', 'DT', 'pkgdown', 'servr',
  'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'ranger', 'future', 'future.apply', 'testthat', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fda', 'spam'

Packages suggested but not available for checking: 'pomp', 'maxLik'

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.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'viridis', 'susieR'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'imager', 'magick', 'shiny', 'scales'

Packages suggested but not available for checking:
  'testthat', 'shinytest', 'covr', 'rmarkdown', 'devtools', 'shinyBS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rcartocolor', 'testthat', 'rmarkdown', 'covr', 'vdiffr'
Running examples in ‘colorblindcheck-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: palette_bivariate_plot
> ### Title: Plot Bivariate Palette And Its Color Vision Deficiencies
> ### Aliases: palette_bivariate_plot
> 
> ### ** Examples
> 
> palette_bivariate_plot(x = rcartocolor::carto_pal(4, "Sunset"))
Error in loadNamespace(x) : there is no package called ‘rcartocolor’
Calls: palette_bivariate_plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'cowplot'

Packages suggested but not available for checking: 'reshape2', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'htmltools', 'testthat', 'dplyr', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ape', 'plotly', 'gplots', 'scales', 'qpdf', 'spatstat.geom'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'testthat', 'covr', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'treemap', 'dplyr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'ggplot2', 'raster', 'scales', 'tidyr'

Packages suggested but not available for checking:
  'rmarkdown', 'sf', 'rnaturalearth', 'tigris'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magick', 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'V8', 'stringr', 'ggplot2'

Packages suggested but not available for checking: 'scales', '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', '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:
  'plotly', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:

  Warning: 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'FNN', 'plyr', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'kernlab', 'shiny', 'shinyjs', 'ggplot2', 'dplyr', 'scales',
  'rmarkdown', 'rcartocolor', 'scico', 'viridis'
Running examples in ‘colorspace-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_binned_diverging
> ### Title: HCL-Based Binned Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_binned_diverging scale_color_binned_diverging
> ###   scale_fill_binned_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Errors in running code in vignettes:
when running code in ‘hcl-colors.Rnw’
  ...

> options(prompt = "R> ", continue = "+  ")

> library("colorspace")

> library("vcd")
Loading required package: grid

> library("mvtnorm")

> library("kernlab")

  When sourcing ‘hcl-colors.R’:
Error: there is no package called ‘kernlab’
Execution halted

  ‘hcl-colors.Rnw’ using ‘UTF-8’... failed
Note: skipping ‘colorspace.Rmd’ due to unavailable dependencies: 'ggplot2'
Note: skipping ‘hcl-colors.Rnw’ due to unavailable dependencies: 'kernlab'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rgl', 'rmarkdown', 'arrangements'

Package which this enhances but not available for checking: ‘plyr’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'httptest', 'testthat', 'vdiffr'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ggplot2', 'htmltools', 'htmlwidgets', 'miniUI', 'shiny', 'shinyjs'

Packages suggested but not available for checking:
  'rmarkdown', 'shinydisconnect'

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: 'rmarkdown', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'covr', 'scales', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'rgl'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'kableExtra', 'shiny', 'shinyjs', 'ggplot2', 'scales', 'rmarkdown'
Package required but not available: ‘Rfast2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Packages required but not available: 'igraph', 'clusterSim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Packages required but not available: 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'spelling', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'tidyr', 'dplyr', 'ggplot2', 'pROC', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'rjags', 'SAMBA'

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘digest’

Packages suggested but not available for checking:
  'covr', 'httptest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'splines2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'ggplot2', 'stringr', 'tidyr', 'RcppArmadillo',
  'RcppEigen', 'RcppNumerical'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggnewscale', 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'pheatmap', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'xml2'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Packages required but not available:
  'Rcpp', 'GGally', 'useful', 'ggplot2', 'reshape2', 'plyr', 'scales',
  'igraph', 'RcppArmadillo'

Packages suggested but not available for checking:
  'qpdf', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringi’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', '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: ‘ROCR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'pcalg', 'InvariantCausalPrediction', 'glmnet', 'backShift', 'CAM',
  'kernlab', 'testthat', 'huge', 'flare'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'copula', 'ggplot2', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'htmlTable', 'openxlsx', 'tidyr', 'stringr'

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'HardyWeinberg', 'rmarkdown', 'kableExtra', 'flextable', 'officer'

Packages suggested but not available for checking:
  'shiny', 'shinyBS', 'shinyjs', 'shinyjqui', 'shinythemes',
  'shinyWidgets', 'shinydashboardPlus', 'DT', 'readxl', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nimble', 'ggplot2', 'reshape2'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'rjags', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CEEMDANML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'plyr', 'testthat', 'covr', 'GauPro', 'ggplot2', 'GGally', 'ggpubr',
  'rmarkdown', 'reshape', 'lhs', 'DiceOptim', 'reshape2'
Running examples in ‘comparer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: R6_hype
> ### Title: Hyperparameter optimization
> ### Aliases: R6_hype
> 
> ### ** Examples
> 
> 
> # Have df output, but only use one value from it
> h1 <- hype(
+   eval_func = function(a, b) {data.frame(c=a^2+b^2, d=1:2)},
+   extract_output_func = function(odf) {odf$c[1]},
+   a = par_unif('a', -1, 2),
+   b = par_unif('b', -10, 10),
+   n_lhs = 10
+ )
Error in loadNamespace(x) : there is no package called ‘lhs’
Calls: hype ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘CVglasso’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'bio3d', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'comperes', 'dplyr', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', '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:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'rhandsontable', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/compHclust.Rcheck/00install.out’ for details.
Packages required but not available: 'car', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Benchmarking', 'spdep', 'Hmisc', 'nonparaeff', 'np', 'FactoMineR',
  'GWmodel'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'lubridate', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggforce', 'ggplot2', 'reshape2'
Running ‘complex_rlm.R’ [0s/1s]
Running the tests in ‘tests/complex_rlm.R’ failed.
Complete output:
  > ####
  > #### William Ryan
  > #### 12 September, 2021
  > #### Test script for complex robust linear fit (rlm).
  > #### Modified from rlm in MASS.
  > #### Test script based on Wuber's answer on stackexchange https://stats.stackexchange.com/questions/66088/analysis-with-complex-data-anything-different#
  > ####
  > 
  > 
  > library(complexlm)
  Loading required package: MASS
  
  Attaching package: 'complexlm'
  
  The following objects are masked from 'package:MASS':
  
      psi.bisquare, psi.hampel, psi.huber, rlm
  
  The following objects are masked from 'package:stats':
  
      cor, cov, lm, lm.fit, lm.wfit, mad, mahalanobis, var
  
  The following object is masked from 'package:base':
  
      range
  
  > library(MASS, include.only = "mvrnorm")
  > library(ggplot2)
  Error in library(ggplot2) : there is no package called 'ggplot2'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'patchwork', 'scales'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'R.rsp', 'laGP'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lme4', 'plyr', 'reshape2', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'codalm', 'Directional', 'energy', 'glmnet', 'mixture', 'mvhtests',
  'pchc', 'regda', 'Rfast', 'Rfast2', 'Rnanoflann'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bayesm’

Packages suggested but not available for checking:
  'rgl', 'energy', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CompQuadForm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'seqinr', 'ggplot2', 'reshape2', 'mixtools', 'igraph', 'heatmap3',
  'TopDom', 'tidyverse', 'ggrepel'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'bookdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'dplyr'
'LazyData' is specified without a 'data' directory
Running examples in ‘con2lki-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: con2lki
> ### Title: Calculate lki from contaminants
> ### Aliases: con2lki
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ape', 'dplyr', 'igraph', 'readxl', 'stringr'

Packages suggested but not available for checking:
  'DT', 'rmarkdown', 'tidyverse', 'testthat'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'V8', '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: 'Rcpp', 'rgl', 'Rvcg'

Package suggested but not available for checking: ‘rmarchingcubes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'trackeR', 'SiZer'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'origami', 'SuperLearner', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'xgboost', 'glmnet', 'ranger', 'ggplot2', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'devtools', 'kableExtra', 'ggplot2',
  'testthat', 'covr'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’
checkRd: (-1) concstats_hhi.Rd:13: Lost braces; missing escapes or markup?
    13 | value is required. Ranges from {0, 1} and often used for comparison over
       |                                ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Errors in running code in vignettes:
when running code in ‘concstats-intro.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘concstats-start.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘concstats-intro.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘concstats-start.Rmd’ using ‘UTF-8’... failed to complete the test
Packages required but not available: 'CompQuadForm', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'data.tree', 'wdm'

Packages suggested but not available for checking: 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fs’

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', 'htmlTable', 'htmltools', 'openxlsx', 'rmarkdown', 'scales'

Packages suggested but not available for checking:
  'promises', 'shiny', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > withr::with_package("testthat", {
  +     testthat::test_check("condGEE")
  + })
  Error in (get("library"))(package, pos = pos, lib.loc = lib.loc, character.only = character.only,  : 
    there is no package called 'testthat'
  Calls: <Anonymous> ... suppressPackageStartupMessages -> withCallingHandlers -> <Anonymous>
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'RPtests', 'caTools', 'kernlab'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BayesFactor', 'shiny'

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'kernlab', 'tidyverse', 'survminer'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'np', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'roxygen2', 'spelling', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘tests.R’ [0s/1s]
Running the tests in ‘tests/tests.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'htmltools', 'shiny'

Packages suggested but not available for checking: 'shinytest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bigrquery’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'ggplot2', 'scales', 'plyr'

Packages suggested but not available for checking:
  'rmarkdown', 'hdrcde', 'keras', 'kernlab', 'ks', 'parsnip', 'mlr',
  'C50', 'bartMachine', 'BART', 'caret', 'e1071', 'gbm', 'glmnet',
  'glmnetUtils', 'mlr3', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'hdrcde', 'gplots', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr', 'spelling'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'RcppTOML', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'prettydoc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘memoise’

Packages suggested but not available for checking:
  'covr', 'dplyr', 'pkgload', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'miniUI', 'rmarkdown', 'shiny', 'stringi', 'xml2'

Packages suggested but not available for checking: 'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstantools’

Packages suggested but not available for checking:
  'rstanarm', 'brms', 'testthat', 'ggplot2', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'fda', 'future', 'future.apply', 'ggplot2', 'ggnewscale', 'ggpubr',
  'scales'

Package suggested but not available for checking: ‘roahd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'future', 'future.apply', 'ggplot2', 'glmnet', 'hrbrthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘e1071’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2', 'repr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) coversim.Rd:103: Lost braces; missing escapes or markup?
   103 | \item{xlas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}},
       |                        ^
checkRd: (-1) coversim.Rd:106: Lost braces; missing escapes or markup?
   106 | \item{ylas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}},
       |                        ^
checkRd: (-1) crplot.Rd:77: Lost braces; missing escapes or markup?
    77 | \item{xlas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}}).}
       |                        ^
checkRd: (-1) crplot.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{ylas}{numeric in {0, 1, 2, 3} specifying the style of axis labels (see \code{las} in \code{\link{par}}).}
       |                        ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘gmp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘penalized’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'tidyr', 'caret', 'furrr'

Packages suggested but not available for checking:
  'rmarkdown', 'e1071', 'scales', 'FeatureTerminatoR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'httptest2', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Ternary’

Packages suggested but not available for checking:
  'ape', 'bookdown', 'phangorn', 'Quartet', 'rmarkdown', 'TreeSearch',
  'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'stringr', 'miceadds'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'ggplot2', 'dplyr', 'genefilter', 'ggrepel', 'gplots',
  'plyr', 'tidyr', 'Hmisc'

Packages suggested but not available for checking:
  'kableExtra', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fpc', 'broom', 'ggplot2', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'Rcpp', 'fixest', 'lwgeom', 's2', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'waiter', 'shinyWidgets', 'summarytools',
  'stringr', 'dplyr', 'Hmisc', 'openxlsx', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'fs'

Packages suggested but not available for checking:
  'flexdashboard', 'ggplot2', 'htmltools', 'lubridate', 'rmarkdown',
  'spelling', 'testthat', 'rsconnect', 'webshot2', 'covr', 'mockery',
  'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rmgarch', 'rugarch', 'igraph', 'glmnet', 'riskParityPortfolio'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pins', 'dplyr', 'dbplyr'

Packages suggested but not available for checking:
  'RSQLite', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qgraph’

Packages suggested but not available for checking:
  'covr', 'lintr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmlwidgets', 'reactable', 'dplyr', 'htmltools', 'digest',
  'crosstalk', 'reactR', 'bslib', 'sass'

Packages suggested but not available for checking:
  'lintr', 'rmarkdown', 'testthat', 'webmockr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘igraph’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'igraph', 'cowplot', 'ComplexHeatmap', 'dendextend', 'dplyr',
  'ggplot2', 'ggrepel', 'leidenAlg', 'N2R', 'reshape2', 'Rtsne',
  'sccore', 'Rcpp', 'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking:
  'AnnotationDbi', 'BiocParallel', 'conosPanel', 'DESeq2', 'ggrastr',
  'GO.db', 'org.Hs.eg.db', 'org.Mm.eg.db', 'p2data', 'pagoda2', 'PMA',
  'plyr', 'rhdf5', 'rmarkdown', 'rmumps', 'Seurat', 'shinycssloaders',
  'testthat', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'kableExtra', 'Rcpp', 'stringr',
  'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'cowplot', 'GGally', 'ggplot2', 'ggrepel', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running 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', 'DiagrammeR', 'rmarkdown', 'covr', 'stringi'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'DiagrammeR', 'shiny', 'shinydashboard', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘coneproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ConsRank', 'janitor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgl', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'nloptr', 'FME', 'MCMCpack', 'GA', 'GenSA', 'ggplot2',
  'adaptMCMC', 'Rcpp'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'units', 'quantities', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'devtools', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

Packages suggested but not available for checking:
  'DiagrammeR', 'DiagrammeRsvg', 'dm', 'dplyr', 'ggplot2', 'lubridate',
  'rmarkdown', 'scales', 'sf', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'StanHeaders', 'RcppEigen',
  'RcppParallel'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'spelling', 'testthat', 'covr'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'dplyr', 'testthat'
Packages required but not available: 'mixture', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fs’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr', 'thor', 'vroom', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'quanteda', 'text2vec', 'reshape2', 'fastDummies',
  'stringr', 'tidyr', 'ggplot2'

Packages suggested but not available for checking: 'hunspell', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rmpfr', 'go2bigq', 'gmp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > testthat::test_check("contingencytables")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'geometry', 'Rcpp', 'reshape', 'plyr'

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:
  'rmarkdown', 'lhs', 'ggplot2', 'laGP', 'covr', 'testthat'
checkRd: (-1) cf_grid.Rd:38: Lost braces; missing escapes or markup?
    38 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) cf_highdim.Rd:58: Lost braces; missing escapes or markup?
    58 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
checkRd: (-1) gcf_grid.Rd:51: Lost braces; missing escapes or markup?
    51 | heat.colors, terrain.colors, topo.colors, and function(x) {gray((1:x)/x)}.}
       |                                                           ^
Running examples in ‘ContourFunctions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cf
> ### Title: Make contour plot from data or function
> ### Aliases: cf
> 
> ### ** Examples
> 
> cf(function(x){x[1]^2 - x[2]})
> x <- runif(20)
> y <- runif(20)
> z <- exp(-(x-.5)^2-5*(y-.5)^2)# + rnorm(20,0,.05)
> cf(x,y,z)
Error in loadNamespace(x) : there is no package called ‘laGP’
Calls: cf ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘interp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rms’

Packages suggested but not available for checking:
  'kableExtra', 'dplyr', 'ggplot2', 'tidyr', 'rmarkdown', 'testthat',
  'covr', 'geepack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rjags', 'devtools', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'ggplot2', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'prettydoc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'orthoDr', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggplot2', 'dplyr', 'riskRegression'

Packages suggested but not available for checking:
  'pammtools', 'gganimate', 'transformr', 'plotly', 'reshape2',
  'rmarkdown', 'testthat', 'vdiffr', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'pryr', 'extraDistr', 'dplyr', 'tidyr', 'ggplot2', 'SHELF', 'shiny'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'ggplot2', 'eurostat', 'tidyr', 'caTools', 'broom',
  'stringr', 'rmarkdown', 'ggpubr', 'leaflet'

Packages suggested but not available for checking:
  'devtools', 'formattable', 'kableExtra', 'readr', 'readxl',
  'tidyverse', 'rvest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AnnotationDbi', 'org.Hs.eg.db', 'org.Mm.eg.db', 'plyr', 'stringr',
  'biomaRt', 'xml2', 'BiocFileCache'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'miniUI', 'DT'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'geiger', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'vardpoor', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fields', 'StatMatch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'gmp', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BiasedUrn', 'cowplot', 'ggplot2', 'plyr', 'reshape'

Package suggested but not available for checking: ‘cooccur’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fs', 'readr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringi', 'urltools'

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clock', 'htmltools', 'httpuv', 'shiny'

Packages suggested but not available for checking:
  'covr', 'pkgdown', 'rmarkdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'pROC', 'plyr', 'ggplot2', 'ClustGeo', 'RcppArmadillo'

Packages suggested but not available for checking: 'ggtree', 'imager'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'rgl'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'GameTheory', 'dplyr', 'kappalab'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'geosphere', 'ggplot2', 'rgbif', 'rnaturalearth', 'terra'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'sf', 'testthat', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RcppSimdJson', 'lubridate', 'igraph', 'stringi'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lmomco’

Package suggested but not available for checking: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mcmcse', 'Rcpp', 'spam', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'copula', 'copBasic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'rmarkdown', 'fitbitViz', 'tmap', 'leaflet', 'leafgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'leaflet', 'readr', 'rvest', 'sf', 'stringr', 'tidyr',
  'xml2'

Packages suggested but not available for checking:
  'ncmeta', 'stars', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'coloc', 'ggplot2', 'ggrepel', 'pheatmap', 'viridis',
  'dplyr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'dirichletprocess', 'RcppArmadillo'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'pcaMethods', 'CVXR', 'ggplot2', 'dplyr', 'tidyr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cordillera', 'smacof', 'minqa', 'crs', 'nloptr', 'rgenoud', 'GenSA'

Packages suggested but not available for checking: 'R.rsp', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rvinecopulib’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'copBasic', 'copula', 'flexsurv', 'icenReg', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'ggplot2', 'plyr', 'reshape2'

Packages suggested but not available for checking:
  'Rmisc', 'bayesplot', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'copula', 'vines'

Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rvinecopulib’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pcaPP’

Packages suggested but not available for checking:
  'Rmpfr', 'rmarkdown', 'lcopula', 'mev', 'partitions', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rvinecopulib’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mc2d’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'testthat', 'energy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'seqinr', 'stringr', 'kmer', 'DECIPHER', 'beepr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'Rtsne'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/coRanking.Rcheck/00install.out’ for details.
Package required but not available: ‘htmltools’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'CRF', 'igraph'

Packages suggested but not available for checking:
  'rmarkdown', 'BiocParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dbscan’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘pcaPP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'testthat', 'vcfR', 'adegenet', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'igraph', 'oro.dicom', 'plyr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'StatMatch'
Running ‘test.R’ [0s/0s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ExplainPrediction’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CORElearn.Rcheck/00install.out’ for details.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: 'car', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'nloptr', 'GenSA', 'phangorn', 'viridis', 'Rmpfr', 'igraph',
  'phytools'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'gplots', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plyr', 'Rdisop'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'detectseparation', 'scales'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr', 'R.rsp', 'optimx', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'SpatialTools'

Packages suggested but not available for checking:
  'ggplot2', 'prettydoc', 'rmarkdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'palasso'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

Packages which this enhances but not available for checking:
  'xgboost', 'MLmetrics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'gganimate', 'ggplot2', 'qicharts2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

Packages suggested but not available for checking:
  'DT', 'dplyr', 'plotly', 'readr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'later', 'promises', 'reticulate', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'padr', 'plyr', 're2', 'rmarkdown',
  'scales', 'shiny', 'shinydashboard', 'shinyjs', 'shinyWidgets',
  'stringi', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'shinytest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'wordcloud', 'stringi', 'Rcpp', 'udpipe', 'digest', 'quanteda',
  'igraph', 'tokenbrowser', 'RNewsflow', 'rsyntax'

Packages suggested but not available for checking:
  'testthat', 'tm', 'topicmodels', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'mmand'

Packages suggested but not available for checking:
  'rmarkdown', 'R.rsp', 'testthat', 'rgl', 'profr'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geepack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'rmarkdown', 'testthat', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'digest', 'rmarkdown', 'xcms', 'xml2'
Packages suggested but not available for checking:
  'rmarkdown', 'pkgdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rgl', 'gplots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'recipes', 'plotly', 'dplyr', 'tidyr', 'ggrepel',
  'stringr'

Packages suggested but not available for checking:
  'scales', 'rmarkdown', 'covr', 'lubridate', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesFactor', 'energy', 'ggplot2', 'ggraph', 'gt', 'Hmisc', 'lme4',
  'rmarkdown', 'rstanarm', 'see', 'testthat', 'tidygraph', 'wdm',
  'WRS2'
Running ‘testthat.R’ [0s/1s]
Running 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: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'visNetwork', 'ingredients', 'htmltools', 'ggplot2'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'DALEX', 'gbm', 'ranger', 'spelling', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rmarkdown', 'prettydoc', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'ggplot2', 'ggrepel'

Packages suggested but not available for checking:
  'covr', 'dbplyr', 'rmarkdown', 'RSQLite', 'sparklyr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'visNetwork', 'plotly', 'gganimate', 'igraph', 'ggraph',
  'GGally', 'shiny'

Packages suggested but not available for checking: 'rmarkdown', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'forecast', 'hts', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # file corset/tests/testthat.R
  > # Copyright (C) 2016 Merck Sharp & Dohme Corp. a subsidiary of Merck & Co.
  > # , Inc., Kenilworth, NJ, USA.
  > #
  > # This program is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # This program is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with this program.  If not, see <http://www.gnu.org/licenses/>.
  > 
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'igraph', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'gplots', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggcorrplot', 'ggpubr', 'ggplot2'

Packages suggested but not available for checking:
  'covr', 'papaja', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nloptr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cosinor', 'cowplot', 'scales', 'stringr', 'ggplot2', 'Hmisc'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'ICAMS', 'usethis'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
Packages required but not available:
  'ggplot2', 'nloptr', 'MBA', 'cowplot', 'animation', 'ggquiver'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rglpk', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'OpenMx', 'ctsem', 'MBESS', 'openxlsx', 'zcurve', 'scholar',
  'stringi'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tram', 'mlt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘colordistance’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'lamW', 'maxLik', 'miscTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmltools', 'prismatic'

Packages suggested but not available for checking:
  'rmarkdown', 'shiny', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'StatMatch', 'iml', 'paradox', 'miesmuschel', 'bbotk'

Packages suggested but not available for checking:
  'GGally', 'trtf', 'testthat', 'R.rsp', 'cowplot', 'covr', 'ggplot2',
  'keras', 'rchallenge', 'rmarkdown', 'mlr3', 'mlr3learners',
  'mlr3pipelines', 'tidymodels', 'caret', 'mlr'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'shiny'

Packages suggested but not available for checking:
  'dplyr', 'DT', 'pander', 'reshape2', 'rmarkdown', 'shinythemes',
  'shinycssloaders', 'shinyWidgets', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'tidyverse', 'viridis', 'igraph', 'RSpectra', 'rdist', 'Seurat',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘compositions’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fasttrakg.Rd:18: Lost braces
    18 |     \item{\code{killip}}{Killip level of cardiac event severity (1-4)age75}{1= Age>75; 0=Age<=75}
       |                                                                            ^
Packages required but not available:
  'tidyr', 'stringr', 'dplyr', 'lubridate', 'ggplot2', 'viridis'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'flexsurv', 'optimx', 'car', 'dplyr', 'standardize',
  'RcppArmadillo'

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: 'eurostat', 'testthat'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ## Test `countrycode` using the `testthat` package
  > 
  > ## Setup
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dbarts', 'FastGP', 'gbm', 'spikeSlabGAM', 'splines2', 'Rcpp',
  'TruncatedNormal', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'bayesplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fastDummies', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'TMB', 'rjags', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lubridate', 'V8', 'gstat', 'spacetime'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'plyr', 'qgraph', 'igraph'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'glmnet', 'latex2exp', 'Rcpp', 'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourpicker', 'egg', 'ggplot2', 'shiny'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'shinyjs', 'shinymeta', 'table1', 'rmarkdown',
  'mrgsolve', 'GGally', 'ggridges', 'ggrepel', 'ggstance', 'patchwork',
  'plotly', 'scales', 'shinyAce', 'Rcpp', 'ggdist', 'ggh4x', 'ggpmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'autothresholdr', 'dplyr', 'lubridate', 'mgc', 'terra', '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: ‘tokenizers’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readxl', 'ape', 'plotly', 'htmlwidgets', 'gplots', 'pheatmap',
  'shiny', 'shinydashboard', 'shinycssloaders', 'DT', 'dplyr',
  'collapsibleTree'

Packages suggested but not available for checking:
  'devtools', 'roxygen2', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'dplyr'

Packages suggested but not available for checking: 'rmarkdown', '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:
  'ggrepel', 'kableExtra', 'leaflet', 'plotly', 'rmarkdown',
  'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'data.tree', 'DT', 'networkD3'
Packages required but not available:
  'dplyr', 'lubridate', 'readr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'EpiEstim', 'gt', 'janitor', 'scales', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

Packages suggested but not available for checking:
  'readr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'RSQLite', 'wbstats'
Packages required but not available:
  'devtools', 'dplyr', 'lubridate', 'mapview', 'plotly', 'sf'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'readr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'snakecase', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'sf', 'tidyr', 'xml2'

Packages suggested but not available for checking:
  'httptest', 'mockery', 'rmarkdown', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'readxl', 'survey'

Packages suggested but not available for checking:
  'convey', 'SIPDIBGE', 'srvyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'seqinr', 'stringr', 'ggpubr', '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', 'duckdb', 'fs', 'pins', 'readr', 'readxl', 'stringr',
  'tidyr'

Packages suggested but not available for checking:
  'covr', 'cowplot', 'dbplyr', 'EpiEstim', 'ggformula', 'ggplot2',
  'ggstream', 'ggtext', 'lubridate', 'MetBrewer', 'rmarkdown',
  'scales', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2'
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running 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:
  'rmarkdown', 'stringi', 'devtools'
Running examples in ‘covidsymptom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_latest_data
> ### Title: Retrieve updated COVID Symptom Study Sweden (CSSS) data
> ### Aliases: get_latest_data
> 
> ### ** Examples
> 
> df <- get_latest_data(data_level = "county")
Error in loadNamespace(x) : there is no package called ‘stringi’
Calls: get_latest_data ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘digest’

Packages suggested but not available for checking:
  'rmarkdown', 'htmltools', 'DT', 'testthat', 'xml2', 'memoise',
  'mockery', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘np’

Package suggested but not available for checking: ‘bindata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rvinecopulib', 'Rcpp'

Packages suggested but not available for checking:
  'rmarkdown', 'R.rsp', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'shapes', 'SHT', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'rgl'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'scales'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'magick', 'PASWR', 'patchwork', 'rmarkdown', 'ragg',
  'testthat', 'tidyr', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'randomForestSRC', 'tidyr', 'ranger', 'gbm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rms', 'dplyr', 'tidyr', 'ggplot2', 'mediation'

Packages suggested but not available for checking: 'rmarkdown', 'bindrcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'is.R' is deprecated.
  Warning: 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MESS', 'qvalue'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'doRNG', 'ggplot2', 'dplyr', 'tikzDevice', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dbscan', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'e1071'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qvalue’
checkRd: (-1) Sample.data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sample.data.Rd:21: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'mvnfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlr3', 'knockoff'

Packages suggested but not available for checking:
  'BEST', 'mlr3learners', 'ranger', 'glmnet', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'minqa', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rms', 'Hmisc', 'benchmarkme'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spelling', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cpm.Rcheck/00install.out’ for details.
Packages required but not available: 'crops', 'Rcpp', 'ggplot2'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'decor', 'ggplot2', 'lobstr', 'mockery', 'rmarkdown',
  'scales', 'Rcpp', 'testthat'
Running examples in ‘cpp11-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cpp_register
> ### Title: Generates wrappers for registered C++ functions
> ### Aliases: cpp_register
> 
> ### ** Examples
> 
> # create a minimal package
> dir <- tempfile()
> dir.create(dir)
> 
> writeLines("Package: testPkg", file.path(dir, "DESCRIPTION"))
> writeLines("useDynLib(testPkg, .registration = TRUE)", file.path(dir, "NAMESPACE"))
> 
> # create a C++ file with a decorated function
> dir.create(file.path(dir, "src"))
> writeLines("[[cpp11::register]] int one() { return 1; }", file.path(dir, "src", "one.cpp"))
> 
> # register the functions in the package
> cpp_register(dir)
Error: The decor package(s) are required for this functionality
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'htmlwidgets', 'rmarkdown', 'shiny', 'V8', 'xml2'

Packages suggested but not available for checking:
  'htmltools', 'shinyAce', 'shinybusy', 'shinyFiles', 'shinyjqui',
  'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cppdoubles.Rcheck/00install.out’ for details.
Packages required but not available: 'kappalab', 'mc2d'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppParallel'

Packages suggested but not available for checking: 'rmarkdown', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'car', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'lme4', 'Rcpp', 'scales', 'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'qwraps2', 'rmarkdown', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available:
  'Rcpp', 'Rfast', 'dplyr', 'tidyr', 'ggplot2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'plyr', 'Hmisc'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'rmarkdown', 'survey', 'srvyr', 'scales', 'ggplot2', 'usmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'Rfast'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'broom', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'patchwork', 'latex2exp', 'tidyr', 'ape'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'xml2', 'rvest', 'stringr', 'dplyr', 'igraph', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'visNetwork', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSQLite’

Packages suggested but not available for checking:
  'covr', 'mockery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'visNetwork', 'igraph', 'stringr', 'ggplot2', 'wordcloud', 'tm'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'shiny', 'shinyjs', 'miniUI', 'stringr', 'DT', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'NMF', 'recommenderlab'
Packages required but not available:
  'Rcpp', 'dplyr', 'sf', 'lubridate', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mockery', 'testthat'
checkRd: (-1) make_style.Rd:51: Lost braces
    51 | The style (the code{...} argument) can be anything of the
       |                    ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(crayon)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘farver’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/crc32c.Rcheck/00install.out’ for details.
Package required but not available: ‘scoringRules’

Package suggested but not available for checking: ‘distributions3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fastglm', 'Rcpp', 'ggplot2', 'ggpubr', 'stringr', 'lme4',
  'reshape2', 'RcppEigen', 'RcppParallel'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Packages suggested but not available for checking:
  'rmarkdown', 'rvest', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'glmnet', 'xgboost'

Packages suggested but not available for checking:
  'pdp', 'pmml', 'gbm', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'ff', 'R.rsp', 'shiny'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'survey', 'ggplot2', 'ggstance', 'scales'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gbm', 'xgboost', 'glmnet', 'bartCause', 'stringr', 'SuperLearner',
  'ggplot2', 'inTrees'

Packages suggested but not available for checking:
  'grf', 'BART', 'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'paws.common', 'paws.compute', 'paws.management'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xml2’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘local.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'rmarkdown', 'Rglpk'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CRF.Rcheck/00install.out’ for details.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'udpipe', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'janitor', 'lubridate', 'readr', 'rvest', 'stringr',
  'tidyr', 'xml2'

Packages suggested but not available for checking:
  'gghighlight', 'ggplot2', 'ggtext', 'paletteer', 'patchwork',
  'rmarkdown', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'forecast', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'digest', 'dplyr', 'osfr', 'sf', 'stringr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'ggplot2', 'readr', 'scales', 'gt', 'tidyr'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'gbm', 'rtracklayer', 'stringr', 'vtreat', 'shiny', 'DT'

Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'dplyr', 'ggplot2', 'keras', 'reticulate', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'igraph', 'stringr'

Packages suggested but not available for checking:
  'DiagrammeR', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DiagrammeR', 'ggplot2', 'reshape2', 'dplyr', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cowplot', 'dplyr', 'ggbeeswarm', 'ggplot2', 'ggpmisc', 'ggpubr',
  'ggrepel', 'scales', 'sccore', 'sparseMatrixStats', 'tidyr'

Packages suggested but not available for checking:
  'conos', 'pagoda2', 'reticulate', 'rhdf5', 'Seurat', 'SoupX',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'GenSA', 'rjags'

Packages suggested but not available for checking:
  'ggmcmc', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FNN', 'ggplot2', 'gplots', 'pcaPP', 'plyr', 'rrcov'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available:
  'shiny', 'shinydashboard', 'stringr', 'dplyr', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘htmltools’

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘digest’

Packages suggested but not available for checking:
  'miniUI', 'shiny', 'shinyFiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'terra', 'sf', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'dplyr', 'purrrlyr'

Packages suggested but not available for checking:
  'rmarkdown', 'furrr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Packages required but not available: 'dplyr', 'raster', 'sf', 'RJSONIO'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape', 'tidyverse', 'memoise', 'ggplot2', 'cowplot'

Package suggested but not available for checking: ‘fpop’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'tidyr', 'sf', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'geepack', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'clustree', 'dbscan', 'dplyr', 'ggdist', 'ggplot2', 'ggpp',
  'patchwork', 'scales', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat', 'umap', '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:
  'broom', 'covr', 'estimatr', 'furrr', 'future', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'meta', 'netmeta', 'rjags', 'dplyr', 'plyr', 'tidyr', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'Rcpp', 'RcppArmadillo', 'digest'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rmpfr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'flextable', 'officer', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'xml2', 'digest', 'gt', 'expss', 'ggplot2', 'Hmisc',
  'lubridate', 'openxlsx', 'rmarkdown', 'stringi', 'systemfonts',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘htmltools’

Packages suggested but not available for checking:
  'shiny', 'ggplot2', 'testthat', 'sass', 'bslib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'dplyr', 'stringr', 'tidyr', 'igraph', 'ensembldb', 'Rcpp',
  'ggplot2', 'STRINGdb'

Packages suggested but not available for checking:
  'tidygraph', 'ggraph', 'testthat', 'EnsDb.Hsapiens.v86', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'gbm', 'glmnet', 'ranger', 'SIS', 'SuperLearner', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Modeler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fpopw’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringi’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'openVA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'labelled', 'readr', 'readxl'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr', 'r6extended'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                                                                                    ^
checkRd: (-1) confRegCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
Packages required but not available:
  'crunch', 'dplyr', 'ggplot2', 'httptest', 'scales', 'stringr'

Packages suggested but not available for checking:
  'covr', 'spelling', 'vdiffr', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gplots', 'rdist'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## load dependencies
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'testthat', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'dplyr', 'readr', 'digest', 'tidytext'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘np’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'units', 'dplyr', 'mapview'

Packages suggested but not available for checking:
  'mapboxapi', 'tigris', 'tidycensus', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'geepack', 'tidyr', 'dplyr', 'lme4', 'sf',
  'spatstat.geom', 'spatstat.random', 'jagsUI'

Packages suggested but not available for checking:
  'rmarkdown', 'INLA', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'webmockr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httpcache’

Packages suggested but not available for checking:
  'covr', 'crunchy', 'devtools', 'haven', 'httptest', 'lintr',
  'rmarkdown', 'spelling', 'styler', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'crunch', 'shiny', 'httpcache', 'miniUI'

Packages suggested but not available for checking:
  'covr', 'htmltools', 'httptest', 'rmarkdown', 'shinytest',
  'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'stringr', 'lubridate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'DT', 'geosphere', 'marmap', 'shiny', 'shinydashboard',
  'shinyjs', 'stringr', 'swfscDAS'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rfast2’

Package suggested but not available for checking: ‘clusterSEs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'tidyr', 'lubridate', 'plyr'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringi', 'digest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lubridate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'kSamples', 'Rmpfr', 'LambertW', 'gmp'

Packages suggested but not available for checking: 'R.rsp', 'bbotk'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flux’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'cstidy', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggrepel', 'plnr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'scales', 'reshape2', 'Lmoments', 'ggpubr', 'raster'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘exactci’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'dplyr', 'stringr', 'prodlim', 'riskRegression',
  'glmnet', 'caret', 'recipes', 'future', 'furrr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'broom', 'dplyr', 'fs', 'geojsonio', 'ggplot2', 'gt',
  'lubridate', 'readxl', 'reshape2', 'rmarkdown', 'rmapshaper',
  'stringr', 'sf', 'tidyr'
Running examples in ‘csdata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_granularity_geo_to_data_set
> ### Title: Adds granularity_geo to a given data set
> ### Aliases: add_granularity_geo_to_data_set
> 
> ### ** Examples
> 
> library(data.table)
> data <- data.table(location_code = c("norge", "county03", "blah"))
> csdata::add_granularity_geo_to_data_set(data)
Error in loadNamespace(x) : there is no package called ‘stringr’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available:
  'future.apply', 'future', 'progressr', 'symmoments',
  'TruncatedNormal'

Packages suggested but not available for checking:
  'dplyr', 'tidyr', 'prettydoc', 'plotly', 'rmarkdown', 'listviewer',
  'testthat', 'ggplot2', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'fuzzyjoin', 'stringr', 'dplyr', 'ggplot2', 'future', 'furrr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'rmapshaper'

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', 'lubridate', 'stringr', 'ggplot2', 'ggspatial', 'raster',
  'sf', 'dplyr', 'tidyhydat', 'OpenStreetMap', 'rnaturalearth'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'multiApply', 'ClimProjDiags', 'CSTools', 'SPEI', 'lmomco', 's2dv'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2', 'ggrepel', 'leaflet', 'sf'
Running examples in ‘csmaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nor_county_map_bxxxx_default_dt
> ### Title: Maps of Norwegian counties in data.table format
> ### Aliases: nor_county_map_bxxxx_default_dt
> ###   nor_county_map_b2024_default_dt nor_county_map_b2020_default_dt
> ###   nor_county_map_b2019_default_dt nor_county_map_b2017_default_dt
> ###   nor_county_position_geolabels_b2024_default_dt
> ###   nor_county_position_geolabels_b2020_default_dt
> ###   nor_county_position_geolabels_b2019_default_dt
> ###   nor_county_position_geolabels_b2017_default_dt
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # 2024 borders
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ROCR', 'caTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'Hmisc', 'rms', 'forestmodel', 'ggplot2', 'ggpubr',
  'survminer', 'xgboost', 'scales'

Packages suggested but not available for checking: 'rmarkdown', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'reshape2', 'R.cache', 'sf', 'lubridate', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'stringr', 'readr', 'ggplot2', 'haven', 'ggcorrplot'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggraph', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'scales'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'fastcluster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'digest', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'gt', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'testthat', 'readxl', 'lubridate'
Running examples in ‘cstime-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: date_to_calmonth_c
> ### Title: Date -> calmonth (character)
> ### Aliases: date_to_calmonth_c date_to_calmonth_c.default
> ###   date_to_calmonth_c.character date_to_calmonth_c.Date
> 
> ### ** Examples
> 
> date_to_calmonth_c("2021-08-11")
[1] "08"
> date_to_calmonth_c(lubridate::today())
Error in loadNamespace(x) : there is no package called ‘lubridate’
Calls: date_to_calmonth_c ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'easyVerification', 's2dv', 'startR', 'multiApply', 'ClimProjDiags',
  'plyr', 'reshape2', 'ggplot2', 'verification', 'lubridate', 'scales'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'cgam', 'coneproj', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/csvread.Rcheck/00install.out’ for details.
Packages required but not available: 'readr', 'stringr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘intervals’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyMatrix', 'rpivotTable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'rmarkdown', 'huge', 'ggplot2', 'gplots', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'roxygen2', 'rmarkdown', 'testthat'
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘qtl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'fda', 'gdistance'

Packages suggested but not available for checking: 'dismo', 'crawl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SuperLearner', 'tmle', 'glmnet'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Bessel', 'digest', 'Gmedian', 'raster', 'sf', 'terra'

Packages suggested but not available for checking:
  'animation', 'dplyr', 'move', 'rmarkdown', 'suncalc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'jiebaR', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fda’

Package suggested but not available for checking: ‘eegkit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringi', 'stringr'

Packages suggested but not available for checking:
  'ape', 'kableExtra', 'readxl', 'rmarkdown', 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PowerTOST', 'OwenQ', 'rmarkdown'

Package suggested but not available for checking: ‘asciicast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'ctmm', 'slouch', 'ClusterR'

Packages suggested but not available for checking:
  'phytools', 'viridis', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pch’

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xml2', 'nodbi', 'stringi', 'lubridate', 'dplyr', 'V8', 'readr',
  'digest'

Packages suggested but not available for checking:
  'devtools', 'rmarkdown', 'RSQLite', 'R.rsp', 'RPostgres', 'duckdb'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'plotly', 'stringi', 'htmlwidgets'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ctsem', 'OpenMx', 'plyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'plyr', 'RcppParallel', 'rstan', 'rstantools',
  'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'lme4', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'latex2exp', 'tsibble'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'rmarkdown', 'dplyr', 'caret', 'e1071', 'rhandsontable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘Hello.csv’
Packages required but not available: 'shiny', 'shinyAce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'xml2', 'rmarkdown'
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'testthat', 'benchr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'sf', 'stringr', 'tidyr', 'tsibble'

Packages suggested but not available for checking:
  'spelling', 'rmarkdown', 'testthat', 'ozmaps', 'GGally', 'ggrepel',
  'ggforce', 'stars', 'units', 'leaflet', 'plotly', 'crosstalk',
  'concaveman', 'vdiffr', 'sftime', 'patchwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmltools', 'htmlwidgets', 'raster', 'stars'

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seqinr’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'covr', 'dplyr', 'modeldata', 'rmarkdown', 'testthat', 'tidyrules'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘digest’
checkRd: (-1) chi2cub1cov.Rd:18-19: Lost braces
    18 | \item{gama}{gama}{Vector of parameters for the feeling component, with length equal to 2
       |                  ^
Documented arguments not in \usage in Rd file 'chi2cub2cov.Rd':
  ‘covar’

Documented arguments not in \usage in Rd file 'cubpq.Rd':
  ‘summary’

Documented arguments not in \usage in Rd file 'cubshe.Rd':
  ‘makeplot’ ‘summary’

Documented arguments not in \usage in Rd file 'kkk.Rd':
  ‘Vector’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘CUBvignette-knitr.Rnw’ using knitr

Quitting from lines 71-76 [unnamed-chunk-1] (CUBvignette-knitr.Rnw)
Error: processing vignette 'CUBvignette-knitr.Rnw' failed with diagnostics:
there is no package called 'digest'
--- failed re-building ‘CUBvignette-knitr.Rnw’

SUMMARY: processing the following file failed:
  ‘CUBvignette-knitr.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'parsnip', 'Rcpp'

Packages suggested but not available for checking:
  'glmnet', 'reticulate', 'testthat', 'xgboost'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'openxlsx', 'DT', 'lmerTest', 'haven', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'stringi'

Packages suggested but not available for checking: 'memoise', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'ggplot2', 'readr', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages suggested but not available for checking: 'rmarkdown', 'devtools'
Packages required but not available: 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstpm2', 'relsurv', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spelling', 'testthat', 'later', 'rmarkdown', 'httpuv'
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘engine.R’ [0s/0s]
  Comparing ‘engine.Rout’ to ‘engine.Rout.save’ ...4d3
< Using libcurl 8.5.0 with GnuTLS/3.8.3
  Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tidyr', 'readr', 'stringr', 'broom', 'job', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rmarkdown’
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggthemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Packages required but not available: 'Rcpp', 'ddalpha', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'feature', 'geometry', 'hdrcde', 'ks', 'ptinpoly', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qgam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FNN', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'covr', 'dplyr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'rmarkdown'

Packages which this enhances but not available for checking:
  'vdiffr', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'set', 'do'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'ggplot2', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'doRNG', 'rmarkdown', 'pkgmaker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'censable', 'dplyr', 'fs', 'readr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ROCR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'origami', 'dplyr', 'stringr', 'RSpectra', 'ggplot2', 'ggpubr'

Packages suggested but not available for checking:
  'future', 'future.apply', 'testthat', 'rmarkdown', 'covr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tableone’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'gWidgets2', 'RGtk2'
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2', 'ggrepel'
Documented arguments not in \usage in Rd file 'compute_stat.Rd':
  ‘K_0’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'testthat', 'dplyr', 'tidyr', 'ggbeeswarm',
  'covr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'geepack', 'rmarkdown', 'pkgdown'
Running examples in ‘cvGEE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv_gee
> ### Title: Proper Scoring Rules for Generalized Estimating Equations
> ### Aliases: cv_gee
> 
> ### ** Examples
> 
> library("geepack")
Error in library("geepack") : there is no package called ‘geepack’
Execution halted
Packages required but not available: 'ggplot2', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CompQuadForm’

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', 'groupdata2', 'lme4', 'plyr', 'pROC', 'rearrr',
  'recipes', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'e1071', 'furrr', 'ggimage', 'ggnewscale', 'merDeriv',
  'rmarkdown', 'testthat', 'xpectr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'lme4'

Packages suggested but not available for checking:
  'dplyr', 'effects', 'glmmTMB', 'latticeExtra', 'rmarkdown',
  'spelling', 'testthat'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'PMA', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘kernlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'gbm', 'glmnet', 'rmarkdown', 'testthat'
Running examples in ‘cvwrapr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: computeError
> ### Title: Compute CV statistics from a prediction matrix
> ### Aliases: computeError
> 
> ### ** Examples
> 
> set.seed(1)
> x <- matrix(rnorm(500), nrow = 50)
> y <- rnorm(50)
> cv_fit <- kfoldcv(x, y, train_fun = glmnet::glmnet,
+                   predict_fun = predict, keep = TRUE)
Error in loadNamespace(x) : there is no package called ‘glmnet’
Calls: kfoldcv ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'gmp', 'Rmpfr', 'osqp', 'RcppEigen'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'

Packages which this enhances but not available for checking:
  'gurobi', 'rcbc', 'cccp', 'Rglpk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xml2', 'stringi', 'RcppCWB', 'zen4R', 'fs'

Packages suggested but not available for checking:
  'tm', 'tokenizers', 'tidytext', 'testthat', 'rmarkdown', 'aws.s3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgl', 'Rvcg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘optimx’

Packages suggested but not available for checking:
  'dplyr', 'GenSA', 'ggplot2', 'minqa', 'nloptr', 'rmarkdown',
  'stringr', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcpp’
Packages required but not available: 'Rcpp', 'xml2'

Packages suggested but not available for checking:
  'raster', 'leaflet', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'geojsonsf', 'progressr', 'RcppSimdJson', 'readr', 'sf',
  'stringr', 'stringi'

Packages suggested but not available for checking: 'covr', 'od', 'stplanr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'flexsurv', 'lubridate', 'plyr', 'scales'

Packages suggested but not available for checking: 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'Andromeda', 'dplyr', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'readr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'intmap', 'gmp', 'memoise', 'VeryLargeIntegers'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'shiny'

Packages suggested but not available for checking: 'rmarkdown', 'BiocStyle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'copula', 'stringr', 'infotheo', 'ggplot2', 'rgl',
  'viridis', 'plotly', 'cowplot', 'mixR', 'transport'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringi', 'memoise'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Errors in running code in vignettes:
when running code in ‘cyphr.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘data.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘cyphr.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘data.Rmd’ using ‘UTF-8’... failed to complete the test
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘aws.s3’

Packages suggested but not available for checking: 'rmarkdown', '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', 'reshape2', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'igraph', 'cowplot', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'dbplyr', 'readr', 'rmarkdown', 'RSQLite', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'MetBrewer', 'patchwork', 'reshape2', 'reticulate',
  'testthat'

Packages suggested but not available for checking: 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'magick', 'patchwork', 'rgl', 'rmarkdown', 'Seurat', 'SeuratObject',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2', 'scales', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'stringi'

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', 'devtools', 'dplyr', 'FSelector', 'ggplot2', 'ggrepel',
  'infotheo', 'ModelMetrics', 'questionr', 'recipes'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mirt', 'rgl'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'rjson'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘htmlwidgets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'dplyr'

Packages suggested but not available for checking:
  'igraph', 'rmarkdown', 'shiny', 'golem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'htmltools', 'tidyr'

Packages suggested but not available for checking: 'listviewer', 'testthat'

Packages which this enhances but not available for checking:
  'igraph', 'treemap', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'dplyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xml2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rmarkdown’

Packages suggested but not available for checking:
  'roxygen2', 'testthat', 'usethis', 'openxlsx', 'officedown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DAAG’
Package required but not available: ‘latticeExtra’

Packages suggested but not available for checking:
  'lme4', 'rmarkdown', 'bookdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'cowplot', 'tidyr', 'dplyr', 'ggbeeswarm', 'scales',
  'ggsci', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'rmarkdown', 'kableExtra'

VignetteBuilder package required for checking but not installed: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RMariaDB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘janitor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'beepr', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'mockery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'AmesHousing', 'dplyr', 'ggplot2', 'Lahman', 'tidyr'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'e1071', 'DescTools'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggpubr', 'plyr'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘V8’

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', 'fst', 'ggplot2', 'lubridate', 'mixtools', 'readr',
  'readxl', 'sf', 'stringr', 'tidyr', 'vroom'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
Package suggested but not available for checking: ‘rmarkdown’
Package required but not available: ‘V8’

Packages suggested but not available for checking:
  'igraph', 'testthat', 'rmarkdown', 'fastDummies'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dagitty’
Package required but not available: ‘dagitty’

Package suggested but not available for checking: ‘ggdag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'deflateBR', 'dplyr', 'janitor', 'lubridate', 'readr', 'stringr',
  'tidytext'

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: ‘rmarkdown’
Packages required but not available:
  'readr', 'ggplot2', 'scales', 'cowplot', 'rmarkdown', 'reactable'

Packages suggested but not available for checking:
  'covr', 'testthat', 'codemetar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'beepr', 'fs', 'gargle', 'googleCloudStorageR', 'magick', 'pdftools',
  'readtext', 'stringr', 'xml2'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'phylobase', 'ggplot2', 'scales', 'ggtree', 'DAISIE', 'castor'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr', 'diversitree', 'corHMM', 'tidyr',
  'dplyr', 'ggimage'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DDD', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown', 'dplyr', 'ggplot2', 'ggtree',
  'tidytree', 'tidyr', 'ape', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'iBreakDown', 'ingredients'

Packages suggested but not available for checking: 'ranger', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DALEX', 'ggplot2'

Packages suggested but not available for checking:
  'auditor', 'gbm', 'ggrepel', 'iml', 'ingredients', 'lime',
  'localModel', 'mlr', 'mlr3', 'ranger', 'recipes', 'reticulate',
  'rmarkdown', 'stacks', 'xgboost', 'testthat', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FNN', 'MLmetrics', 'caret', 'dbscan', 'dplyr', 'e1071', 'elmNNRcpp',
  'forecast', 'ggplot2', 'reshape', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DALY.Rcheck/00install.out’ for details.
Packages required but not available: 'caret', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caper', 'ape', 'picante', 'DDD', '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:
  'ggplot2', 'reshape2', 'dplyr', 'scales', 'stringr', 'ggrepel'

Packages suggested but not available for checking:
  'testthat', 'lintr', 'rmarkdown', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'testthat', 'covr', 'ggetho', 'zeitgebr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'crul', 'janitor', 'readxl'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘anytime’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dang.Rcheck/00install.out’ for details.
Packages required but not available:
  'ggplot2', 'e1071', 'ggrepel', 'latex2exp', 'scales'

Packages suggested but not available for checking:
  'car', 'caret', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Epi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'stringr', 'fpc', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr', 'dplyr', 'recipes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'dplyr', 'ggplot2', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid package aliases in Rd file 'dap-package.Rd':
  ‘dap-package’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'lubridate', 'stringr', 'tidyr', 'xesreadR', 'bupaR',
  'readr', 'edeaR', 'miniUI', 'shiny'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available:
  'adegenet', 'lfda', 'kernlab', 'klaR', 'plotly', 'rARPACK'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'plyr'

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'ggplot2', 'dplyr', 'dartR.data', 'ape', 'patchwork',
  'plyr', 'reshape2', 'SNPRelate', 'StAMPP', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'dismo', 'gdistance', 'gganimate', 'ggrepel', 'ggthemes',
  'gplots', 'HardyWeinberg', 'hierfstat', 'igraph', 'iterpc',
  'leaflet', 'leaflet.minicharts', 'mmod', 'networkD3', 'pegas',
  'pheatmap', 'plotly', 'poppr', 'qvalue', 'Rcpp', 'rgl', 'rmarkdown',
  'scales', 'seqinr', 'sf', 'shinyBS', 'shinyjs', 'shinythemes',
  'shinyWidgets', 'SIBER', 'stringi', 'terra', 'vcfR', 'viridis',
  'fields', 'testthat', 'ggtern'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'ggplot2', 'patchwork',
  'stringr'

Packages suggested but not available for checking:
  'SIBER', 'gplots', 'fields', 'igraph', 'reshape2', 'scales',
  'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'dplyr', 'patchwork',
  'ggplot2', 'stringr'

Packages suggested but not available for checking:
  'SIBER', 'fields', 'gplots', 'igraph', 'iterpc', 'leaflet', 'plyr',
  'qvalue', 'raster', 'reshape2', 'scales', 'tidyr', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'ggplot2', 'dplyr', 'dartR.data', 'ape', 'fields',
  'patchwork', 'plyr', 'PopGenReport', 'raster', 'reshape2', 'shiny',
  'SNPRelate', 'StAMPP', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'devtools', 'dismo', 'gdistance', 'ggtern', 'gganimate', 'ggrepel',
  'ggthemes', 'gplots', 'HardyWeinberg', 'hierfstat', 'igraph',
  'iterpc', 'leaflet', 'leaflet.minicharts', 'mmod', 'networkD3',
  'pegas', 'pheatmap', 'plotly', 'poppr', 'qvalue', 'Rcpp', 'rgl',
  'rmarkdown', 'scales', 'seqinr', 'shinyBS', 'shinyjs', 'shinythemes',
  'shinyWidgets', 'SIBER', 'stringi', 'terra', 'vcfR', 'viridis',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'ggplot2', 'shiny', 'fields',
  'stringi', 'stringr', 'Rcpp', 'shinyBS', 'shinyjs', 'shinythemes',
  'shinyWidgets', 'hierfstat', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'dartR.base', 'dartR.data', 'StAMPP', 'raster', 'tidyr',
  'ggplot2'

Packages suggested but not available for checking:
  'mmod', 'dismo', 'gdistance', 'gplots', 'terra', 'sf', 'PopGenReport'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dartR.base', 'dartR.data'

Packages suggested but not available for checking:
  'devtools', 'dartR.sim', 'dartR.captive', 'dartR.popgen',
  'dartR.spatial'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘htmltools’

Packages suggested but not available for checking:
  'testthat', 'lintr', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'readr', 'urltools', 'digest', 'dbplyr'

Packages suggested but not available for checking:
  'aws.s3', 'testthat', 'DBItest', 'rmarkdown', 'RSQLite', 'Andromeda',
  'dplyr', 'RPostgres', 'odbc', 'duckdb', 'pool', 'ParallelLogger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'GeneralizedUmatrix', 'RcppArmadillo'

Packages suggested but not available for checking:
  'DataVisualizations', 'rmarkdown', 'geometry', 'spdep', 'rgl',
  'ProjectionBasedClustering', 'parallelDist', 'dendextend'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'rvest', 'stringr', 'magick', 'plyr', 'tidyr'

Packages suggested but not available for checking:
  'av', 'testthat', 'ggplot2', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'htmltools', 'summarytools', 'dplyr', 'DT', 'plotly',
  'lubridate', 'shinyWidgets', 'htmlwidgets', 'fs', 'shinyFiles',
  'bslib'

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: 'devtools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringi'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'admiraldev', 'dplyr', 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'devtools', 'lintr', 'pkgdown', 'testthat', 'rmarkdown', 'roxygen2',
  'spelling', 'styler', 'usethis', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'haven', 'labelled', 'lubridate', 'openxlsx', 'tidyr'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'anytime', 'dplyr', 'lubridate', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyBS', 'shinyjs', 'bslib', 'rhandsontable', 'htmltools',
  'miniUI'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'scales', 'ggplot2', 'rmarkdown', 'networkD3'

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidygraph', 'dplyr'

Packages suggested but not available for checking:
  'stringr', 'stringi', 'rmarkdown', 'covr', 'lintr', 'mockery',
  'testthat', 'rcmdcheck'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'openxlsx', 'dplyr', 'plyr', 'tidyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'GA', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'pander', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readxl', 'plyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'haven', 'htmltools', 'pander', 'rmarkdown', 'stringi'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'lubridate'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmltools', 'htmlwidgets', 'phosphoricons', 'reactable', 'readxl',
  'rio', 'shiny', 'shinyWidgets', 'shinybusy'

Packages suggested but not available for checking:
  'bslib', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'dplyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringi', 'stringr', 'datapack', 'plyr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'digest', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'digest', 'fs', 'redland'

Packages suggested but not available for checking:
  'testthat', 'igraph', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lubridate', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'scales', 'dplyr', 'reshape2'

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'lme4', 'lubridate', 'patchwork', 'reshape',
  'rio', 'scales'

Packages suggested but not available for checking:
  'anytime', 'cowplot', 'digest', 'DT', 'flexdashboard',
  'flexsiteboard', 'htmltools', 'rmarkdown', 'testthat', 'vdiffr',
  'pkgload', 'plotly', 'ggvenn', 'htmlwidgets', 'future', 'shiny',
  'summarytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'haven', 'htmltools', 'pander', 'rmarkdown', 'stringi'

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', 'rmarkdown'
Running examples in ‘dataresqc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_decimals
> ### Title: Plot decimals
> ### Aliases: plot_decimals
> 
> ### ** Examples
> 
> plot_decimals(Rosario$Tx, outfile = paste0(tempdir(),"/test.pdf"))
Error: Package "ggplot2" needed for this function to work. Please install it.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lubridate', 'xml2', 'readr'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'DT', 'rmarkdown', 'sf', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lubridate', 'testthat', 'lintr', 'AmesHousing', 'doBy', 'rmarkdown',
  'ggplot2', 'memoise'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘Multiclass.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘tidyr’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'RSDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘jsonvalidate’

Packages suggested but not available for checking:
  'testthat', 'haven', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dataspice', 'covr', 'dplyr', 'eurostat', 'kableExtra', 'rdflib',
  'readxl', 'rmarkdown', 'spelling', 'testthat', 'tidyr', 'tsibble'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'shiny', 'miniUI', 'DT'

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rlabkey', 'digest'

Packages suggested but not available for checking:
  'testthat', 'covr', 'pryr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'EML', 'fs', 'readr', 'stringr', 'shiny', 'rhandsontable', 'dplyr',
  'tidyr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'kableExtra', 'rmarkdown', 'servr', 'listviewer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringi', 'stringr', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'rjson'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'scales'

Package suggested but not available for checking: ‘ROCnReg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringi’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ape', 'networkD3', 'treemap',
  'htmlwidgets', 'DiagrammeR', 'mockery'

Package which this enhances but not available for checking: ‘igraph’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'assertr', 'shiny.semantic', 'dplyr', 'tidyr', 'rmarkdown',
  'htmltools', 'htmlwidgets'

Packages suggested but not available for checking:
  'covr', 'fixtuRes', 'fs', 'lintr', 'rcmdcheck', 'readr', 'shiny',
  'spelling', 'targets', 'testthat', 'visNetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'dplyr', 'dbplyr', 'duckdb', 'RSQLite', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'readr', 'xml2'

Packages suggested but not available for checking:
  'covr', 'haven', 'rmarkdown', 'testthat', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'plyr', 'MBA', 'ggmap', 'rworldmap', 'rgl', 'choroplethr', 'dplyr',
  'parallelDist', 'rmarkdown', 'ggExtra', 'plotly', 'htmlwidgets',
  'ggrepel', 'ScatterDensity', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'dplyr', 'gamm4', 'ggplot2', 'gt', 'haven', 'htmltools',
  'lme4', 'mediation', 'readxl', 'readr', 'rio', 'rmarkdown',
  'rstanarm', 'see', 'testthat', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'Hmisc', 'janitor', 'readr', 'readxl', 'sf', 'sidrar',
  'stringi', 'stringr', 'tidyr', 'Rcpp'

Packages suggested but not available for checking:
  'googledrive', 'rmarkdown', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'stringr'

Packages suggested but not available for checking:
  'DT', 'htmltools', 'readxl', 'rmarkdown', 'shiny', 'shinytest2',
  'spelling', 'testthat', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'bold', 'phangorn', 'phytools', 'ips', 'geiger', 'stringr',
  'rotl', 'paleotree', 'knitcitations', 'phylobase', 'taxize',
  'treebase', 'plyr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'usethis', 'devtools', 'covr', 'msa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmltools', 'jsonify', 'shiny'

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘clock’

Packages suggested but not available for checking:
  'lubridate', 'nanotime', 'parttime', 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmltools', 'lubridate', 'reactR', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'lubridate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'Lahman', 'modeldata', 'tidyr'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'devtools', 'dplyr', 'ggplot2', 'ggridges', 'reshape2',
  'rmarkdown', 'stringr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘aoos’

Packages suggested but not available for checking:
  'dplyr', 'lintr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'odbc', 'dplyr', 'RSQLite'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Errors in running code in vignettes:
when running code in ‘dawai.Rnw’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder 'R.rsp' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘dawai.Rnw’... failed to complete the test
Packages required but not available: 'sf', 'terra', 'tidyr'

Packages suggested but not available for checking:
  'ggplot2', 'dplyr', 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping vignette re-building
Packages suggested but not available for checking: 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dbarts.Rcheck/00install.out’ for details.
Packages required but not available:
  'caret', 'TSdist', 'ggplot2', 'parallelDist', 'plyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RSQLite’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readxl', 'tidyr', 'dplyr', 'ggplot2', 'pander', 'rmarkdown',
  'questionr', 'labelled', 'naniar'

Package suggested but not available for checking: ‘testthat’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidypredict', 'tidyverse', 'dbplyr', 'dplyr', 'tidyr', 'stringr'

Packages suggested but not available for checking:
  'RSQLite', 'duckdb', 'bigrquery', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'seqHMM', 'TraMineR', 'reshape2', '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: ‘reshape2’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'covr', 'DBItest', 'dbplyr', 'downlit', 'dplyr',
  'nanoarrow', 'RMariaDB', 'rmarkdown', 'RSQLite', 'testthat', 'xml2'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'lubridate', 'nanoarrow', 'testthat'

Packages suggested but not available for checking:
  'constructive', 'devtools', 'dplyr', 'lintr', 'pkgload', 'rmarkdown',
  'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘xgboost’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
Packages required but not available:
  'Rcpp', 'spatstat.explore', 'cubature', 'ggplot2', 'RcppParallel',
  'reshape2', 'spatstat.geom', 'spatstat.random'

Packages suggested but not available for checking:
  'testthat', 'pkgdown', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bnviewer', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘NMF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'visNetwork', '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: 'rmarkdown', 'testthat'

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:
  'dbplyr', 'testthat', 'tidyr', 'covr'

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:
  'covr', 'Lahman', 'odbc', 'RMariaDB', 'rmarkdown', 'RPostgres',
  'RSQLite', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'GBJ'

Packages suggested but not available for checking: 'bindata', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MfUSampler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'fpc', 'testthat', 'dendextend', 'igraph', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'urltools', 'RSQLite', 'RMariaDB', 'RPostgres', 'odbc'
Running examples in ‘dbx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbxConnect
> ### Title: Create a database connection
> ### Aliases: dbxConnect
> 
> ### ** Examples
> 
> # SQLite
> db <- dbxConnect(adapter="sqlite", dbname=":memory:")
Error in requireLib("RSQLite") : Could not load adapter: RSQLite
Calls: dbxConnect -> findAdapter -> requireLib
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'c3net', 'igraph', 'RedeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘Ecdat’
Running examples in ‘DCchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbchoice
> ### Title: Parametric approach to analyze double-bounded dichotomous choice
> ###   contingent valuation data
> ### Aliases: dbchoice print.dbchoice vcov.dbchoice logLik.dbchoice
> ### Keywords: DCchoice double-bounded nonlinear
> 
> ### ** Examples
> 
> ## Examples are based on a data set NaturalPark in the package 
> ## Ecdat (Croissant 2011): DBDCCV style question for measuring 
> ## willingness to pay for the preservation of the Alentejo Natural 
> ## Park. The data set (dataframe) contains seven variables: 
> ## bid1 (bid in the initial question), bidh (higher bid in the follow-up 
> ## question), bidl (lower bid in the follow-up question), answers 
> ## (response outcomes in a factor format with four levels of "nn", 
> ## "ny", "yn", "yy"), respondents' characteristic variables such 
> ## as age, sex and income (see NaturalPark for details).
> data(NaturalPark, package = "Ecdat")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘Ecdat’
Calls: data -> find.package
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'maxLik', 'rumidas', 'rugarch', 'roll', 'lubridate',
  'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlogit’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyBS', 'shinycssloaders', 'shiny', 'shinyWidgets', 'DT',
  'readxl', 'idefix', 'tidyr', 'mlogit', 'htmltools', 'dfidx',
  'adjustedcranlogs', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'devtools'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'tensorflow', 'BiocParallel', 'dplyr', 'ape', 'phangorn', 'Rcpp',
  'igraph', 'stringr', 'tidyr', 'rBayesianOptimization',
  'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rjags', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spacetime', 'DCluster', 'lme4'

Packages suggested but not available for checking: 'INLA', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phylogram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'modelr', 'Rcpp', 'stringr', 'tidyr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'GDINA', 'roxygen2', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dclone’

Package suggested but not available for checking: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘simplermarkdown’

VignetteBuilder package required for checking but not installed: ‘simplermarkdown’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘seqinr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'Rfast', 'ggplot2', 'pheatmap', 'Hmisc', 'RcppArmadillo',
  'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dcov', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dcov', 'Rfast', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'beepr', 'dplyr', 'janitor', 'tidyr',
  'StanHeaders', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'nnTensor'

Packages suggested but not available for checking: 'rmarkdown', '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: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom', 'dplyr', 'ggplot2', 'scales'

Packages suggested but not available for checking:
  'covr', 'gtsummary', 'rmarkdown', 'spelling', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dtwclust’

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phytools', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking: 'testthat', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'testthat', 'dplyr'
Running examples in ‘ddi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ddc
> ### Title: Data Defect Correlation
> ### Aliases: ddc
> 
> ### ** Examples
> 
> library(tibble)
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘qpdf’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'digest', 'xml2', 'haven', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'glmnet', 'ranger', 'xgboost'

Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
Package required but not available: ‘dbscan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'dplyr', 'ggplot2', 'mixtools', 'plyr', 'readr', 'shiny',
  'shinydisconnect', 'shinyjs'

Packages suggested but not available for checking:
  'ggExtra', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘r2d3’

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggalt', 'MEGENA', 'igraph', 'Hmisc', 'plyr', 'scales'

Packages suggested but not available for checking: 'WGCNA', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'shiny', 'RcppEigen'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'extraDistr', 'ggplot2', 'ggpubr', 'ggtext', 'ggtree',
  'phylobase', 'BayesLogit'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'tidyr', 'plotly', 'igraph', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'aphid', 'seqinr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CVXR', 'caret'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyjs', 'shinydashboard', 'shinydashboardPlus'

Packages suggested but not available for checking: 'R.rsp', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'devtools', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'ggraph', 'igraph', 'rmarkdown', 'roxygen2',
  'scales', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'mockery', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'chillR', 'dplyr', 'ggplot2', 'ggstance', 'patchwork',
  'rriskDistributions', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'mc2d', 'rmarkdown', 'scales', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'htmltools', 'readr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'sf', 'scales', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘estimatr’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'AER', 'dplyr', 'ggplot2', 'future',
  'future.apply', 'broom', 'Matching', 'sf', 'reshape2',
  'DesignLibrary'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'DT', 'testthat', 'rmarkdown', 'tidyr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'keras', 'tensorflow', 'reticulate', 'tsutils', 'Rlibeemd',
  'TSdeeplearning', 'VMDecomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rlibeemd', 'forecast'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'usethis', 'StratigrapheR', 'dplyr'

Packages suggested but not available for checking:
  'EMD', 'Rssa', 'astrochron', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'reshape2', 'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19'

Package suggested but not available for checking: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'rmarkdown'
checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'covr', 'testthat'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/decor.Rcheck/00install.out’ for details.
Packages required but not available:
  'ggplot2', 'car', 'e1071', 'scales', 'plyr', 'effects'

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘editrules’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'reshape2', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘collapse’

Packages suggested but not available for checking:
  'dplyr', 'readr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'kableExtra', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'covr', 'devtools', 'ggplot2', 'ggraph', 'graphlayouts', 'igraph',
  'miniCRAN', 'plyr', 'rmarkdown', 'scales', 'shiny',
  'shinycssloaders', 'spelling', 'stringi', 'testthat', 'vcr'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'fastDummies', 'plyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'GpGp', 'Rcpp', 'FNN', 'RcppArmadillo'

Packages suggested but not available for checking: 'interp', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tokenizers’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'extraDistr', 'dplyr', 'Rfast', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'keras', 'reticulate', 'seqinr',
  'tensorflow'

Packages suggested but not available for checking:
  'covr', 'kableExtra', 'rmarkdown', 'stringr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'tfprobability', 'keras', 'dplyr', 'reticulate',
  'tfruns'

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(deepRstudio)
  > 
  > # Setting
  > options(testthat.use_colours = FALSE)
  > 
  > testthat::test_file("testthat/test_deepRstudio.R")
  Error in loadNamespace(x) : there is no package called 'testthat'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available:
  'ggplot2', 'ggnewscale', 'ggforce', 'scales', 'ggfittext', 'phytools'

Packages suggested but not available for checking:
  'dplyr', 'divDyn', 'ape', 'paleotree', 'dispRity', 'ggtree',
  'testthat', 'vdiffr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tensorflow', 'keras', 'tfprobability', 'deepregression', 'mlt',
  'reticulate'

Packages suggested but not available for checking:
  'testthat', 'tram', 'cotram', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ActivePathways', 'dplyr', 'ggplot2', 'glmnet', 'ggrepel',
  'downloader'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'readxl', 'xml2', 'xslt', 'reporter', 'libr', 'openxlsx'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lubridate'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘memoise’

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'terra', 'plyr', 'StableEstim', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'cimir', 'dplyr', 'testthat', 'tidyr', 'units'
Running examples in ‘degday-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dd_calc
> ### Title: Estimate degree days from daily data
> ### Aliases: dd_calc dd_simp_avg dd_sng_tri dd_sng_sine dd_dbl_tri
> ###   dd_dbl_sine
> 
> ### ** Examples
> 
> daily_temps <- system.file("extdata/espartoa-weather-2020.csv", package = "degday") %>%
+   read.csv() %>%
+     dplyr::mutate(date = as.Date(date)) %>%
+     dplyr::slice(1:10)
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'parglm', 'glmmTMB', 'ggplot2', 'ggpubr', 'ggrepel', 'car', 'dplyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘covr’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'igraph', 'future', 'visNetwork'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘polyclip’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'doRNG', 'ggplot2', 'scales'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyMatrix', 'shinyBS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'reshape2'

Packages suggested but not available for checking:
  'covr', 'lintr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) deming.Rd:71: Lost braces
    71 | on whether the code{cv} option is TRUE or FALSE, respectively.
       |                    ^
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘covr’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'tidyr', 'dplyr', 'GGally'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown', 'dplyr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘officer’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'flextable', 'e1071'

Package suggested but not available for checking: ‘officer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'ftsa', 'rainbow', 'HMDHFDplus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'tidyr', 'igraph'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Rcpp', 'fields', 'spam', 'ClusterR', 'RcppArmadillo'

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:
  'rmarkdown', 'testthat', 'ape', 'gplots', 'heatmaply', 'fpc', 'covr'

Packages which this enhances but not available for checking:
  'ggdendro', 'Hmisc', 'WGCNA', 'distory', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > # Run all tests for gphys package
  > #  
  > # Author: jefferis
  > ###############################################################################
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'reshape2', 'scales', 'oce', 'MLmetrics', 'dplyr',
  'plotly', 'Cubist', 'lubridate', 'viridis', 'dplR'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'gplots', 'gapmap', 'rmarkdown'
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: 'roxygen2', 'tsibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’
Errors in running code in vignettes:
when running code in ‘denoiSeq-vignette.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘denoiSeq-vignette.Rmd’ using ‘UTF-8’... failed to complete the test
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘FactoMineR’

Package suggested but not available for checking: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'reshape2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppArmadillo', 'RcppEigen',
  'RcppParallel', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggdensity', 'isoband', 'sf', 'sfheaders'

Packages suggested but not available for checking:
  'ggplot2', 'ragg', 'readr', 'rmarkdown', 'stringr', 'testthat',
  'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FNN', 'ggplot2', 'ggrepel', 'Rtsne'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'testthat', 'usethis', 'devtools', 'roxygen2', 'ggplot2', 'cowplot',
  'rmarkdown'
Running examples in ‘denvax-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lazou2016
> ### Title: The serosurvey data in L'Azou 2016
> ### Aliases: lazou2016
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(denvax); 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(lazou2016)
> ggplot(lazou2016) + aes(Age, Seropositive/Number*100, color = Country) +
+   geom_point() + labs(y="Seropositive %", x="Age Group") + lims(y=c(0,100)) +
+   theme_minimal()
Error in ggplot(lazou2016) : could not find function "ggplot"
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'copula'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fs', 'ggplot2', 'Hmisc', 'readr', 'rms', 'stringr',
  'telegram.bot', 'tidyr', 'usethis'

Packages suggested but not available for checking:
  'covr', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘Rdonlp2’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/depmix.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) responses.Rd:68: Lost braces
    68 | 	response.  See code{\link{makeDepmix}} for an example of how to use
       |                            ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'sf', 'terra', 'xml2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'Rcpp', 'rrcov', 'np', 'geometry', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rgl', 'dplyr', 'RcppArmadillo', 'covr', 'testthat', 'fda', 'lintr',
  'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping vignette re-building
Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'dplyr', 'tidyr', 'pander', 'bookdown'

VignetteBuilder packages required for checking but not installed:
  'ggplot2', 'dplyr', 'tidyr', 'pander', 'bookdown'
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
Errors in running code in vignettes:
when running code in ‘derivmkts-vignette.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'ggplot2' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘derivmkts-vignette.Rmd’ using ‘UTF-8’... failed to complete the test
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) Deriv.Rd:33: Lost braces
    33 | guessed either from\ code{names(formals(f))} (if \code{f} is a function)
       |                          ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'covr', 'spelling', 'testthat'
Packages required but not available:
  'dplyr', 'tidyr', 'broom', 'stringr', 'haven', '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', 'e1071'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'ggplot2', 'plyr', 'scales', 'GGally'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'testthat', 'lintr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'rmarkdown', 'rmdformats', 'ggpattern', 'paletteer', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'reshape'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'scales', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat', 'vdiffr', 'xplorerr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'exact2x2', 'DescTools', 'dplyr', 'stringr', 'scales', 'kableExtra',
  'flextable', 'officer', 'rmarkdown', 'haven', 'Hmisc'

Packages suggested but not available for checking:
  'testthat', 'covr', 'tidyverse', 'shiny'

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', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'pander', 'dplyr', 'DT', 'htmltools', 'tidyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'gld', 'readxl'

Packages suggested but not available for checking:
  'RDCOMClient', 'R.rsp', 'testthat'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'animation', 'shiny', 'future', 'furrr',
  'future.apply', 'progressr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'badger', 'rmarkdown', 'smoots', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reticulate', 'fields', 'plotly', 'dplyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bs4Dash', 'bslib', 'cicerone', 'fontawesome', 'golem', 'htmltools',
  'shinipsum', 'shiny', 'shinyscreenshot'

Packages suggested but not available for checking:
  'chromote', 'lintr', 'rmarkdown', 'shinytest2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DeclareDesign', 'estimatr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘highs’

Packages which this enhances but not available for checking:
  'gurobi', 'Rglpk', 'Rsymphony'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lme4'

Packages suggested but not available for checking:
  'rmarkdown', 'lmerTest', 'afex', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'spelling', 'testthat'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Packages suggested but not available for checking: 'readxl', 'testthat'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'sitmo'

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FME’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'reshape2'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmltools', 'xml2'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', '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: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'dclone', 'dcmle'
Packages required but not available: 'plyr', 'ggplot2', 'reshape2', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'prettydoc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pkgload’

Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'AER', 'ROI.plugin.glpk', 'ROI.plugin.neos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'pcaPP', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tourr', 'htmlwidgets'

Packages suggested but not available for checking:
  'testthat', 'crosstalk', 'shiny', 'htmltools', 'dplyr', 'liminal',
  'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'autothresholdr', 'dplyr', 'filesstrings', 'ijtiff', 'plyr', 'Rcpp',
  'RcppParallel', 'stringr'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'rmarkdown', 'spelling', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcaPP', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pheatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'shiny', 'DT'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/devEMF.Rcheck/00install.out’ for details.
Packages required but not available: 'plyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘covr’
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'usethis', 'fs', 'memoise', 'miniUI', 'pkgdown', 'pkgload',
  'profvis', 'rcmdcheck', 'roxygen2', 'rversions', 'testthat',
  'urlchecker'

Packages suggested but not available for checking:
  'covr', 'digest', 'DT', 'foghorn', 'gmailr', 'lintr', 'mockery',
  'rhub', 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'DynTxRegime'

Packages suggested but not available for checking: 'dplyr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dexter', 'shiny', 'shinyBS', 'DT', 'htmltools', 'htmlwidgets',
  'shinyjs', 'shinyFiles', 'dplyr', 'tidyr', 'readxl', 'readODS',
  'ggplot2', 'ggExtra', 'ggridges', 'networkD3'

Packages suggested but not available for checking: 'sirt', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'dexter', 'dplyr', 'RSQLite', 'igraph',
  'tidyr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'mirt', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RSQLite', 'tidyr', 'dplyr', 'Rcpp', 'RcppArmadillo', 'dqrng',
  'sitmo'

Packages suggested but not available for checking:
  'rmarkdown', 'latticeExtra', 'testthat', '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: 'rmarkdown', 'prettydoc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BayesFactor', 'MVN'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'rmarkdown', 'bookdown', 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'stringr', 'gprofiler2', 'signatureSearch', 'signatureSearchData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'rmarkdown', 'AER', 'mlogit', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mirt', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'plyr', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘e1071’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'collapse', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcppArmadillo', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplR', 'dplyr', 'ggplot2', 'ggpubr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'rstan', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'ggplot2', 'plotly'

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MLInterfaces', 'genefilter'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WGCNA’

Packages suggested but not available for checking:
  'gplots', 'testthat', 'ggplot2', 'GOstats', 'org.Hs.eg.db',
  'AnnotationDbi', 'MEGENA', 'igraph', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'biomaRt', 'conflicted', 'dplyr', 'edgeR', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DGEobj', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'biomaRt', 'canvasXpress', 'conflicted', 'edgeR', 'ggplot2', 'IHW',
  'qvalue', 'rmarkdown', 'sva', 'testthat', 'zFPKM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'sf', 'Rcpp'

Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'R.rsp', 'testthat'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) AIC.dglars.Rd:47: Lost braces
    47 | \item{comp}{the measures of model complexity used to compute the measure of goodness-of-fit. It is equal to \code{npar} when code{complexity = "df"};}
       |                                                                                                                                  ^
checkRd: (-1) dglars.Rd:258: Lost braces
   258 | 		\item{\code{7}}{maximum number of solution points ('code{np}') reached.}
       |                                                                         ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'nloptr', 'COMPoissonReg'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'reshape2', 'ggplot2', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'reticulate', 'benchmarkme', 'ggplot2', 'ggforce', 'reshape2',
  'patchwork', 'lhs', 'clhs', 'dplyr'

Packages suggested but not available for checking: 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gap', 'ape', 'qgam', 'lme4'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'mgcViz', 'spaMM', 'glmmTMB'

Packages which this enhances but not available for checking:
  'phyr', 'rstan', 'rjags', 'BayesianTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape', 'survey', 'haven', 'dplyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'greekLetters', 'conquer', 'cubature'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'meta', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'htmltools', 'htmlwidgets', 'igraph', 'readr', 'scales',
  'stringr', 'tidyr', 'visNetwork'

Packages suggested but not available for checking:
  'DiagrammeRsvg', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'covr', 'dplyr', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'scales', 'dplyr'

Packages suggested but not available for checking:
  'covr', 'kernlab', 'rmarkdown', 'testthat', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tidyr', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'memoise', 'tidyr'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgl’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'rgenoud', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## load dependencies
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘rgenoud’

Packages suggested but not available for checking: 'KrigInv', 'GPareto'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clusterSim', 'dplyr', 'ggplot2', 'infotheo', 'klaR', 'NMF', 'Rcpp',
  'stringr', 'tidyr', 'yardstick'

Packages suggested but not available for checking:
  'apcluster', 'blockcluster', 'covr', 'dbscan', 'e1071', 'kernlab',
  'kohonen', 'pander', 'rmarkdown', 'Rtsne', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R.cache', 'geometry'

Packages suggested but not available for checking:
  'rlibkriging', 'rgl', 'arrangements'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘matlabr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) DIconvex.Rd:40: Lost braces; missing escapes or markup?
    40 |  {Paul Schneider <paul.schneider@usi.ch>}{}
       |  ^
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) define.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fixest', 'MatrixExtra', 'broom', 'ggplot2', 'did', 'staggered',
  'didimputation'

Packages suggested but not available for checking:
  'rmarkdown', 'haven', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'igraph', 'stringi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'scales', 'fixest'
Running examples in ‘DiDforBigData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DiD
> ### Title: Combine DiD estimates across cohorts and event times.
> ### Aliases: DiD
> 
> ### ** Examples
> 
> # simulate some data
> simdata = SimDiD(sample_size=200, ATTcohortdiff = 2)$simdata
> 
> # define the variable names as a list()
> varnames = list()
> varnames$time_name = "year"
> varnames$outcome_name = "Y"
> varnames$cohort_name = "cohort"
> varnames$id_name = "id"
> 
> # estimate the ATT for all cohorts at event time 1 only
> DiD(simdata, varnames, min_event=1, max_event=1)
Loading required namespace: fixest
Failed with error:  ‘there is no package called ‘fixest’’
[1] "warning: fixest not found"
Error in str2lang(x) : <text>:2:0: unexpected end of input
1: Y_diff ~ -1 + treated_2007 + treated_2010 + treated_2012 + 
   ^
Calls: DiD ... as.formula -> formula -> formula.character -> str2lang
Execution halted
Packages required but not available:
  'fixest', 'Rcpp', 'broom', 'dplyr', 'stringr', 'tidyr',
  'RcppArmadillo'

Packages suggested but not available for checking: 'haven', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'fixest', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BMisc', 'ggplot2', 'ggpubr', 'DRDID', 'tidyr'

Packages suggested but not available for checking:
  'rmarkdown', 'plm', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vcfR’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rfishbase’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘penalized’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gplots', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcaMethods', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'lubridate', 'rmarkdown', 'dplyr', 'stringi', 'stringr',
  'devtools', 'covr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'arrow', 'dplyr', 'janitor'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'pcaPP'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'stringr', 'reshape2', 'ggnewscale'

Packages suggested but not available for checking:
  'rmarkdown', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘JuliaCall’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BoolNet', 'DOT', 'igraph'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'ggplot2', 'tidyr', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages suggested but not available for checking:
  'randomNames', 'testthat', 'rmarkdown'
checkRd: (-1) sensitivitySamplerManual-DPMech-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual-DPMechNumeric-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual.Rd:22: Lost braces
    22 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bernstein.Rnw’ using knitr
--- finished re-building ‘bernstein.Rnw’

--- re-building ‘diffpriv.Rnw’ using knitr

Quitting from lines 296-310 [samplerExponential] (diffpriv.Rnw)
Error: processing vignette 'diffpriv.Rnw' failed with diagnostics:
there is no package called 'randomNames'
--- failed re-building ‘diffpriv.Rnw’

SUMMARY: processing the following file failed:
  ‘diffpriv.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘htmlwidgets’

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggdendro', 'ggplot2', 'igraph', 'Rcpp', 'reshape2', 'viridis',
  'RcppEigen'

Packages suggested but not available for checking:
  'cowplot', 'parallelDist', 'strex', 'tidyr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nloptr', 'systemfit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘htmlwidgets’

Packages suggested but not available for checking: 'covr', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pander’

Packages suggested but not available for checking:
  'Ckmeans.1d.dp', 'FunChisq', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'penalized', 'miscTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'calculus', 'ggplot2', 'plyr'

Package suggested but not available for checking: ‘ShinyItemAnalysis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'TestDataImputation', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mirt', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'difR', '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: ‘penalized’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘simplermarkdown’

VignetteBuilder package required for checking but not installed: ‘simplermarkdown’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/digest.Rcheck/00install.out’ for details.
Packages required but not available:
  'tidyr', 'readr', 'dplyr', 'ggplot2', 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'zinbwave', 'dplyr', 'reshape2', 'reticulate', 'keras',
  'tensorflow', 'ggplot2', 'ggpubr'

Packages suggested but not available for checking:
  'rmarkdown', 'BiocParallel', 'rhdf5', 'DelayedMatrixStats',
  'HDF5Array', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'BeyondBenford', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'viridis', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bibliometrix', 'rmarkdown'
Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'svglite', 'tinysnapshot'
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) DIME.Rd:272: Lost braces; missing escapes or markup?
   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
Packages required but not available:
  'DImodels', 'plyr', 'dplyr', 'reshape2'

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'testthat'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DRR’

Packages suggested but not available for checking:
  'NMF', 'RANN', 'RSpectra', 'Rtsne', 'cccd', 'coRanking',
  'diffusionMap', 'energy', 'ggplot2', 'igraph', 'keras', 'kernlab',
  'optimx', 'pcaPP', 'reticulate', 'rgl', 'scales', 'tensorflow',
  'testthat', 'tidyr', 'umap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'biomaRt', 'plyr'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'simcdm', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'CDM', 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'covr', 'ggplot2', 'lubridate', 'rmarkdown', 'scales', 'testthat'
scale_date_ym: no visible binding for global variable ‘date_ym_trans’
scale_date_yq: no visible binding for global variable ‘date_yq_trans’
scale_date_yw: no visible binding for global variable ‘date_yw_trans’
Undefined global functions or variables:
  date_ym_trans date_yq_trans date_yw_trans
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'WGCNA', 'ggplot2'

Package suggested but not available for checking: ‘edgeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'usethis', 'ggplot2', 'lemon', 'dplyr', 'e1071'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'shiny', 'stringr', 'future', 'future.apply', 'progressr',
  'fastmap', 'digest'

Packages suggested but not available for checking:
  'promises', 'later', 'rmarkdown', 'testthat', 'future.callr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'mvnfast', 'rlemon'

Packages suggested but not available for checking: 'optmatch', 'rrelaxiv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘scales’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'reshape2', 'scales', 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'bigstatsr', 'ggplot2', 'Rfast', 'Rfast2', 'Rnanoflann', 'rgl',
  'rnaturalearth', 'sf'

Package suggested but not available for checking: ‘bigreadr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'alphahull', 'latticeExtra', 'dplyr', 'ggthemes',
  'testthat'
Packages required but not available: 'collapsibleTree', 'data.tree'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'haven', 'Rcpp', 'lbfgs', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'EdSurvey'

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', 'rmarkdown', 'tidyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘maxLik’

Packages suggested but not available for checking:
  'rgl', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mcmcse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rotasym’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'expectreg', 'nloptr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'TMB', 'dplyr', 'ggplot2', 'cowplot', 'fmesher', 'tidyterra',
  'terra', 'sf', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'INLA', 'rmarkdown', 'SpatialEpi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'shiny', 'shinytest2', 'testthat', 'vdiffr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'tidyr', 'Rcpp', 'rstan', 'SHELF', 'ggplot2',
  'RcppParallel', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'rmarkdown', 'rstantools', '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: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'TSCAN', 'igraph', 'ggplot2', 'fpc', 'AnnotationDbi', 'org.Hs.eg.db'

Packages suggested but not available for checking: 'testthat', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'testthat', 'disclapmix', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'ggplot2', 'ggdendro', 'scales', 'fwsim', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'lubridate', 'pdftools', 'qdap', 'SentimentAnalysis',
  'stringi', 'stringr', 'syuzhet', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sirt', 'cubature', 'copula'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'GGally', 'ggplot2', 'ggrepel', 'igraph'

Packages suggested but not available for checking:
  'ggpubr', 'R.rsp', 'rmarkdown', 'rticles', 'testthat'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr', 'stringi', 'tm'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'golem', 'shiny', 'plotly', 'loadeR', 'ggplot2', 'shinyjs',
  'shinyAce', 'ggdendro', 'echarts4r', 'htmltools', 'FactoMineR',
  'htmlwidgets', 'colourpicker', 'shinydashboard', 'shinycustomloader',
  'shinydashboardPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'igraph', 'RcppEigen'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'R.rsp', 'rmarkdown', 'discreteMTP'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'cvmdisc', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

Packages suggested but not available for checking: 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'parsnip', 'dials'

Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'klaR', 'modeldata', 'rmarkdown',
  'sparsediscrim', 'spelling', 'testthat', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rmdformats’

Packages suggested but not available for checking: 'dfidx', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geepack', 'ranger', 'mvnfast'

Packages suggested but not available for checking: 'caret', 'Ecdat', 'pec'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stm', 'stringr', 'tm'

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:
  'rmarkdown', 'terra', 'sf', 'tmap', 'mapview'
Packages required but not available:
  'dbplyr', 'dplyr', 'lintr', 'lubridate', 'readr', 'SCDB', 'stringr',
  'tidyr'

Packages suggested but not available for checking:
  'devtools', 'rmarkdown', 'RSQLite', 'RPostgres', 'testthat',
  'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'fst', 'duckdb', 'stringr', 'collapse'

Packages suggested but not available for checking:
  'rmarkdown', 'prettydoc', 'ggplot2', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'Rcpp', 'future.apply', 'fs', 'pryr', 'stringr', 'fst',
  'future', 'bigreadr', 'benchmarkme', 'arrow'

Packages suggested but not available for checking:
  'shiny', 'LaF', 'readr', 'broom', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'Rcpp', 'terra'

Packages suggested but not available for checking:
  'ROCR', 'gstat', 'kernlab', 'gbm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘digest’

Packages suggested but not available for checking:
  'mvp', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'covr', 'testthat'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'lubridate'

Packages suggested but not available for checking:
  'devtools', 'rmarkdown', 'roxygen2', 'testthat', 'covr', 'tidyr',
  'skimr', 'ggplot2', 'ggridges', 'furrr', 'future'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'ade4', 'castor', 'Claddis', 'geometry', 'GET', 'phangorn',
  'phyclust', 'phylolm', 'scales'

Packages suggested but not available for checking: 'MCMCglmm', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'biomartr', 'dplyr', 'RSQLite', 'stringr', 'seqinr'
checkRd: (-1) store_in_DB.Rd:89: Lost braces
    89 | link{read_from_DB} function. Those parameters define rows and columns that will be returned.
       |     ^
checkRd: (-1) unite_two_DF.Rd:46: Lost braces; missing escapes or markup?
    46 | \code{data1.shared.var} and {data2.shared.var} must contain unique values within its own data frame.
       |                             ^
Running examples in ‘disprose-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: count_PhCh
> ### Title: Calculate physical and chemical properties
> ### Aliases: count_PhCh count_GC count_REP count_MFE count_TM
> 
> ### ** Examples
> 
> probes <- data.frame (ids = 1:3,  probes = c ("acacacacacaca", "aaaaagggggtttttccccc",
+                                              "atgcgctagctcagc"))
> probes <- count_GC (probe.var = probes$probes, trim.gc = FALSE, GCmin = 40, GCmax = 60,
+                    add.to.data = TRUE, data = probes)
Error: Package "stringr" needed for this function to work. Please install it.
Execution halted
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'caret', 'raster', 'plyr', 'dplyr', 'viridis'

Packages suggested but not available for checking: 'rmarkdown', 'Cubist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'mrds', 'dplyr'

Packages suggested but not available for checking:
  'covr', 'doRNG', 'testthat', 'optimx', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/distances.Rcheck/00install.out’ for details.
Packages required but not available: 'sf', 'nabor'

Packages suggested but not available for checking:
  'fasterize', 'rmarkdown', 'raster', 'lwgeom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'fields', 'viridis', 'arrangements'

Packages suggested but not available for checking:
  'devtools', 'kableExtra', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'readxl', 'dplyr', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'digest', 'stringr', 'dplyr', 'homomorpheR', 'gmp'

Packages suggested but not available for checking:
  'opencpu', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Packages required but not available:
  'ggplot2', 'glmnet', 'Rforestry', 'dplyr', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bookdown', 'digest', 'downlit', 'htmltools', 'lubridate',
  'rmarkdown', 'stringr', 'xml2'

Packages suggested but not available for checking:
  'covr', 'DiagrammeR', 'htmlwidgets', 'r2d3', 'rsconnect', 'shiny',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fs', 'Rcpp', 'RcppParallel', 'usethis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'factoextra', 'ggplot2', 'broom', 'fastcluster'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourpicker', 'dplyr', 'DT', 'extraDistr', 'ggplot2', 'rio',
  'scales', 'shiny', 'shinyalert', 'shinyBS', 'shinyjs',
  'shinyWidgets', 'stringi', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'bamlss', 'ggplot2', 'rhandsontable'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'learnr', 'rmarkdown', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'scales', 'farver', 'digest'

Packages suggested but not available for checking:
  'testthat', 'covr', 'ggdist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'GA', 'AdaptGauss'

Package suggested but not available for checking: ‘parallelDist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'covr', 'cowplot', 'revdbayes', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'tidyverse', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) moranTest.Rd:37: Lost braces; missing escapes or markup?
    37 |   {M(theta)=-(log(y_1-y_0)+log(y_2-y_1)+...+log(y_m-y_m-1))}
       |   ^
Skipping checking math rendering: package 'V8' unavailable
Package which this enhances but not available for checking: ‘RobExtremes’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘ROptEst’

Package which this enhances but not available for checking: ‘RobAStBase’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘digest’

Packages suggested but not available for checking:
  'covr', 'dplyr', 'dbplyr', 'odbc', 'RMariaDB', 'RPostgres',
  'RSQLite', 'spelling', 'testthat', 'rmarkdown', 'lintr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'cowplot', 'ggrepel', 'ggridges'

Packages suggested but not available for checking:
  'plotly', 'testthat', 'ggplot.multistats', 'ggrastr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'rmarkdown', 'icosa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geosphere', 'plotly', 'uniReg'

Packages suggested but not available for checking: 'pander', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FME’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggmulti', 'loon.ggplot', 'loon.shiny', 'loon.tourr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'pheatmap', 'igraph', 'entropart'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp'

Packages suggested but not available for checking:
  'minqa', 'lubridate', 'caper', 'geiger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'ggpubr', 'scales', 'rms', 'MapGAM', 'RcppEigen'

Packages suggested but not available for checking: 'testthat', 'BOLTSSIRR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'unmarked', 'dplyr', 'ggplot2', 'qpcR', 'raster'

Packages suggested but not available for checking: 'rgdal', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RNifti'

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BAT', 'SESraster', 'terra'

Packages suggested but not available for checking:
  'ape', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'dplyr', 'tidyr', 'stringr', 'ggplot2', 'plotly',
  'pryr', 'kableExtra'

Packages suggested but not available for checking:
  'flexdashboard', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'dplyr', 'units'

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: 'iNEXT', 'sf', 'terra', 'units'

Packages suggested but not available for checking:
  'rnaturalearth', 'ggplot2', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spatstat.geom', 'spatstat'

Package suggested but not available for checking: ‘ecespa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lintr', 'shiny', 'shinyjs', 'testthat'
Running examples in ‘DIZtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clear
> ### Title: Clean the console and environment-variables.
> ### Aliases: clear
> 
> ### ** Examples
> 
> clear()
Error: Please install the 'glue' package to use clear
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'Hmisc', 'RJSONIO', 'RPostgres', 'xml2'

Packages suggested but not available for checking: 'lintr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat', 'httptest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'nardl', 'dynlm', 'AER', 'plyr', 'roll'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'SAM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'MSEtool', 'dplyr', 'ggplot2', 'Rcpp', 'TMB', 'RcppEigen'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'geepack'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'digest', 'fs'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'scales'

Packages suggested but not available for checking:
  'tidyr', 'DT', 'rmarkdown', 'prettydoc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) dma.Rd:47: Lost braces; missing escapes or markup?
    47 | When y_t is controlled, only y_{t-delay-1} and before 
       |                                ^
checkRd: (-1) dma.Rd:64: Lost braces; missing escapes or markup?
    64 | 		 estimate of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:66: Lost braces; missing escapes or markup?
    66 | 		 variance of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:68: Lost braces; missing escapes or markup?
    68 | 		 estimate of theta_{j-1} at t}
       |                                    ^
checkRd: (-1) dma.Rd:70: Lost braces; missing escapes or markup?
    70 | 		 variance of thetahat_{j-1} at t}
       |                                       ^
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'bayesplot', 'ggplot2', 'ggrepel', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'lme4'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gbm', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lfda’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'stringr', 'plyr', 'dplyr'

Packages suggested but not available for checking:
  'reticulate', 'pander', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'igraph', 'memoise', 'tidyr'

Packages suggested but not available for checking:
  'colourpicker', 'covr', 'dbplyr', 'DiagrammeR', 'DiagrammeRsvg',
  'digest', 'duckdb', 'htmltools', 'htmlwidgets', 'labelled', 'odbc',
  'pool', 'reactable', 'RMariaDB', 'rmarkdown', 'RPostgres', 'RSQLite',
  'shiny', 'shinyAce', 'shinydashboard', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hclust1d', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet', 'kernlab', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'readxl', 'lubridate', 'tidyr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRaven', 'gRbase'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'igraph', 'ggplot2', 'SeqNet', 'dplyr', 'wCorr',
  'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'xml2', 'readr', 'bc3net', 'DWLasso',
  'huge', 'GENIE3', 'minet', 'AnnotationDbi', 'reactome.db', 'biomaRt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'multicool', 'Rcpp', 'RcppParallel'

Packages suggested but not available for checking:
  'testthat', 'testthis', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flare’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rvest', '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:
  'igraph', 'spdep', 'GOstats', 'caTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'igraph', 'arm', 'glmnet'

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: ‘MCMCpack’
S3 methods shown with full name in Rd file 'add.joint.mean.many.Rd':
  ‘all.cond.mean.PO’ ‘all.cond.mean2.PO’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Argument items with no description in Rd file 'derivType.Rd':
  ‘L’ ‘mu’ ‘eps’
Argument items with no description in Rd file 'getNewParams.SC.Rd':
  ‘n.fft’
Argument items with no description in Rd file 'graph.CTMC.Rd':
  ‘\dots’
Argument items with no description in Rd file 'num.deriv.Rd':
  ‘\dots’
Argument items with no description in Rd file 'power.coef.one.Rd':
  ‘\dots’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dbscan', 'ggplot2'

Packages suggested but not available for checking:
  'rmarkdown', 'OutliersO3', 'FNN'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) beetle.Rd:13: Lost braces; missing escapes or markup?
    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
Packages required but not available:
  'broom', 'dplyr', 'ggplot2', 'pbkrtest'

Packages suggested but not available for checking:
  'geepack', 'lme4', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tm', 'quanteda', 'glmnet', 'stringr', 'textstem', 'stringi'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'tokenizers.bpe', 'word2vec', 'uwot', 'dbscan', 'udpipe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fs', 'memoise', 'usethis'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Packages suggested but not available for checking:
  'rmarkdown', 'R.rsp', 'stringr'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'magick', 'pdftools'

Packages suggested but not available for checking: 'testthat', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'copula', 'cubature', 'testthat'
'LazyData' is specified without a 'data' directory
Running examples in ‘docopulae-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nint_integrateNCube
> ### Title: Integrate Hypercube
> ### Aliases: nint_integrateNCube nint_integrateNCube_integrate
> ###   nint_integrateNCube_cubature nint_integrateNCube_SparseGrid
> 
> ### ** Examples
> 
> ## integrate with defaults (stats::integrate)
> nint_integrate(sin, nint_space(nint_intvDim(pi/4, 3*pi/4)))
[1] 1.414214
> 
> 
> dfltNCube = nint_integrateNCube
> 
> ## prepare for integrateA
> ncube = function(f, lowerLimit, upperLimit, ...) {
+     cat('using integrateA\n')
+     integrateA(f, lowerLimit, upperLimit, ..., subdivisions=2)
+ }
> ncube = nint_integrateNCube_integrate(ncube)
> unlockBinding('nint_integrateNCube', environment(nint_integrate))
> assign('nint_integrateNCube', ncube, envir=environment(nint_integrate))
> 
> ## integrate with integrateA
> nint_integrate(sin, nint_space(nint_intvDim(pi/4, 3*pi/4)))
using integrateA
[1] 1.414214
> 
> 
> ## prepare for cubature
> ncube = function(f, lowerLimit, upperLimit, ...) {
+     cat('using cubature\n')
+     r = cubature::adaptIntegrate(f, lowerLimit, upperLimit, ..., maxEval=1e3)
+     return(r$integral)
+ }
> unlockBinding('nint_integrateNCube', environment(nint_integrate))
> assign('nint_integrateNCube', ncube, envir=environment(nint_integrate))
> 
> ## integrate with cubature
> nint_integrate(sin, nint_space(nint_intvDim(pi/4, 3*pi/4)))
using cubature
Error in loadNamespace(x) : there is no package called ‘cubature’
Calls: nint_integrate ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'parsermd', 'quanteda', 'quanteda.textstats', 'stringr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘roxygen2’

Packages suggested but not available for checking: 'devtools', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fs', 'pkgload', 'roxygen2', 'testthat'

Packages suggested but not available for checking: 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'officer', 'htmltools'

Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rcmdcheck', 'roxygen2'

Packages suggested but not available for checking:
  'pkgload', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'ggplot2', 'lubridate', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xml2', 'dplyr'

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'digest', 'fs', 'osmdata', 'Rcpp', 'RcppParallel', 'RcppThread'

Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'igraph', 'rmarkdown', 'roxygen2', 'sf',
  'testthat', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘partitions’

Packages suggested but not available for checking: 'FrF2', 'DoE.wrapper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DoE.base’

Package which this enhances but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'FrF2', 'DoE.base', 'lhs'

Package suggested but not available for checking: ‘skpr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'future', 'future.apply'

Packages suggested but not available for checking: 'doRNG', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggthemes', 'igraph', 'qpdf', 'rmarkdown'

Packages suggested but not available for checking:
  'testthat', 'devtools', 'tidyr', 'networkD3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arrow', 'reticulate'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'lme4', 'relaimpo', 'rmarkdown', 'stringr',
  'systemfit', 'testthat', 'tidyr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'nabor', 'RANN', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'igraph', 'Morpho', 'rgl', 'Rvcg', 'concaveman', 'usethis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Packages required but not available: 'dplyr', 'stringr', 'tidytext'

Packages suggested but not available for checking:
  'rmarkdown', 'conflicted', 'readr', 'rvest', 'sqldf', 'tidyr',
  'testthat', 'usethis', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'tmcn', 'reshape2', 'tidyr', 'rvest', 'xml2', 'usethis',
  'stringr', 'openxlsx'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘redux’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'ggplot2', 'lmerTest'

Packages suggested but not available for checking:
  'rmarkdown', 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rngtools’

Packages suggested but not available for checking:
  'doRedis', 'devtools', 'testthat', 'pkgmaker', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sensitivity2x2xk', 'senstrat'

Packages suggested but not available for checking: 'optmatch', 'DiPs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'dagitty', 'DOT', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'DT', 'latticeExtra', 'ggplot2', 'shinyjs', 'stringr',
  'shinyWidgets', 'DoseFinding', 'shinyBS', 'readxl', '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:
  'rmarkdown', 'testthat', 'RBesT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'tidyr', 'dplyr', 'ggplot2', 'prettydoc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘optmatch’
Packages suggested but not available for checking: 'rmarkdown', 'rms'
Error(s) in re-building vignettes:
  ...
--- re-building ‘dosresmeta.Rnw’ using knitr

Quitting from lines 330-331 [loading.rms] (dosresmeta.Rnw)
Error: processing vignette 'dosresmeta.Rnw' failed with diagnostics:
there is no package called 'rms'
--- failed re-building ‘dosresmeta.Rnw’

SUMMARY: processing the following file failed:
  ‘dosresmeta.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'plyr', 'testthat'
Running examples in ‘dostats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dostats
> ### Title: Convenient interface for computing statistics on a vector
> ### Aliases: dostats
> ### Keywords: misc utilities
> 
> ### ** Examples
> 
> data(mtcars)
> library(plyr)
Error in library(plyr) : there is no package called ‘plyr’
Execution halted
Running ‘test_package.R’ [0s/0s]
Running the tests in ‘tests/test_package.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'roxygen2', 'spam', 'testthat'
Running ‘run-all.R’ [0s/1s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > require("RhpcBLASctl"); omp_set_num_threads(1)
  Loading required package: RhpcBLASctl
  > # to address:
  > # * checking tests ... [10s/1s] NOTE
  > #   Running ‘run-all.R’ [10s/1s]
  > #   Running R code in ‘run-all.R’ had CPU time 10.5 times elapsed time
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) dot.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘V8’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'rmapshaper', 'sf', 'terra', 'dplyr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'wacolors'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyr', 'stringr', 'dplyr', 'ggplot2', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'stringr', 'ggstance'

Packages suggested but not available for checking: 'rmarkdown', 'broom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘coneproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mlr3', 'mlr3tuning', 'readstata13', 'mlr3learners', 'mlr3misc'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr', 'patrick', 'paradox', 'dplyr',
  'glmnet', 'ranger', 'AER', 'bbotk', 'mlr3pipelines'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) PMLE.Weibull.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.Weibull.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
checkRd: (-1) PMLE.loglogistic.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.loglogistic.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
checkRd: (-1) PMLE.lognormal.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.lognormal.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'covr'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'kableExtra', 'stringi', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'digest', 'memoise'

Packages suggested but not available for checking:
  'covr', 'htmltools', 'pkgload', 'rmarkdown', 'testthat', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘digest’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fs', 'readr', 'bsplus', 'htmltools', 'ggplot2'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'spelling', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cubature', 'Rmpfr', 'sf', 'terra'

Packages suggested but not available for checking:
  'rgbif', 'rmarkdown', 'bookdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'alakazam', 'ape', 'dplyr', 'ggtree', 'phangorn',
  'shazam', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', '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: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘digest’

Packages suggested but not available for checking:
  'covr', 'testthat', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dbscan', 'e1071', 'exactci', 'ggplot2', 'ggpubr', 'raster',
  'scales', 'shiny', 'shinyjs', 'stringr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'digest', 'stringi', 'stringr', 'plyr'

Packages suggested but not available for checking:
  'forecast', 'gmp', 'rmarkdown', 'testthat', 'tikzDevice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'miniUI', 'shinyWidgets', 'shinyAce', 'tidyverse', 'tidyr',
  'stringr', 'plyr', 'DT'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'broom', 'covr', 'dbplyr', 'ggplot2', 'Lahman', 'lobstr',
  'rmarkdown', 'RSQLite', 'stringi', 'testthat', 'tidyr'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dplyr.Rcheck/00install.out’ for details.
Packages required but not available: 'panelr', 'stringr', 'dplyr', 'jtools'

Packages suggested but not available for checking:
  'broom', 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'digest', 'rio'

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: 'dplyr', 'nloptr', 'e1071', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rmpfr', 'gmp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Rmpfr', 'DPQmpfr', 'gmp', 'interp'
Running examples in ‘DPQ-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: p1l1
> ### Title: Numerically Stable p1l1(t) = (t+1)*log(1+t) - t
> ### Aliases: p1l1 p1l1. p1l1p p1l1ser .p1l1ser
> 
> ### ** Examples
> 
> t <- seq(-1, 4, by=1/64)
> plot(t, p1l1ser(t, 1), type="l")
> lines(t, p1l1.(t), lwd=5, col=adjustcolor(1, 1/2)) # direct formula
> for(k in 2:6) lines(t, p1l1ser(t, k), col=k)
> 
> ## zoom in
> t <- 2^seq(-59,-1, by=1/4)
> t <- c(-rev(t), 0, t)
> stopifnot(!is.unsorted(t))
> k.s <- 1:12; names(k.s) <- paste0("k=", 1:12)
> 
> ## True function values: use Rmpfr with 256 bits precision: ---
> ### eventually move this to ../tests/ & ../vignettes/log1pmx-etc.Rnw
> #### FIXME: eventually replace with  if(requireNamespace("Rmpfr")){ ......}
> #### =====
> if((needRmpfr <- is.na(match("Rmpfr", (srch0 <- search())))))
+     require("Rmpfr")
Loading required package: Rmpfr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rmpfr’
> p1l1.T <- p1l1.(mpfr(t, 256)) # "true" values
Error in mpfr(t, 256) : could not find function "mpfr"
Calls: p1l1.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
Package suggested but not available for checking: ‘testthat’
Package required but not available: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'htmltools', 'RcppDynProg', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MCMCpack', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'daterangepicker', 'DIZutils', 'DQAstats', 'DT', 'lubridate',
  'shiny', 'shinyalert', 'shinydashboard', 'shinyFiles', 'shinyjs',
  'shinyWidgets', 'waiter'

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:
  'DIZutils', 'future', 'future.apply', 'kableExtra', 'rmarkdown'

Packages suggested but not available for checking:
  'DT', 'lintr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'sitmo'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'sitmo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openxlsx', 'qtl', 'stringr', 'vroom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'drc', 'devtools', 'roxygen2', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'testthat', 'spelling', 'covr'

Package which this enhances but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tidyr', 'dplyr', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'htmlwidgets', 'shiny', 'shinyjs'

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'digest', 'igraph', 'storr'

Packages suggested but not available for checking:
  'clustermq', 'disk.frame', 'downloader', 'fst', 'future', 'ggplot2',
  'ggraph', 'keras', 'lubridate', 'networkD3', 'qs', 'Rcpp',
  'rmarkdown', 'styler', 'testthat', 'usethis', 'visNetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'readr', 'xml2', 'tokenizers', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'highcharter', 'rmarkdown', 'igraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DoubleML', 'glmnet', 'hdi', 'mlr3', 'paradox', 'rjson', 'rmarkdown',
  'testthat', 'xgboost'
Running examples in ‘drape-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: basis_poly
> ### Title: Estimate the score function of the d'th covariate using a
> ###   polynomial basis.
> ### Aliases: basis_poly
> 
> ### ** Examples
> 
> set.seed(0)
> X <- matrix(stats::rnorm(200), ncol=4)
> bs <- basis_poly(X=X, d=1, degree=2)
Error: Package "glmnet" needed for this function to work.
         Please install it.
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping vignette re-building
Package suggested but not available for checking: ‘simplermarkdown’

VignetteBuilder package required for checking but not installed: ‘simplermarkdown’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available:
  'htmltools', 'bsplus', 'shiny', 'stringr'

Packages suggested but not available for checking: 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
Package required but not available: ‘ROCR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'readxl', 'shiny', 'shinycssloaders', 'shinydashboard'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'ade4', 'sde'

Packages suggested but not available for checking:
  'fda', 'ggplot2', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'glmnet'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'drc', 'drcte', 'plyr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'drc', 'plyr', 'dplyr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat'
checkRd: (-1) logistic2_fn.Rd:34: Lost braces; missing escapes or markup?
    34 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
checkRd: (-1) loglogistic2_fn.Rd:35: Lost braces; missing escapes or markup?
    35 | This function allows values other than {0, 1, -1} for \code{alpha} and \code{delta} but
       |                                        ^
Running ‘spelling.R’ [0s/0s]
  Running ‘testdata.R’ [0s/1s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘BMisc’

Packages suggested but not available for checking:
  'rmarkdown', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'dplyr', 'stringr', 'WGCNA', 'Rfast', 'readr', 'tidyr',
  'reticulate'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SuperLearner’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'ggplot2', 'rjags', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'fs', 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringmagic’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fastDummies', 'Rcpp', 'transport', 'RcppEigen'

Package suggested but not available for checking: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'PBSmapping', 'raster', 'spatstat.geom', 'spatstat.linnet',
  'spatstat', 'spdep'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘learnr’

Packages suggested but not available for checking:
  'rmarkdown', 'scales', 'modelsummary', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DALEX', 'dplyr', 'tidyr', 'ingredients'

Packages suggested but not available for checking: 'testthat', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'seqinr', 'ggplot2', 'future', 'tidyverse', 'dplyr', 'reshape2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rmarkdown', 'devtools', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'caret', 'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Hsapiens.UCSC.hg38.knownGene', 'org.Hs.eg.db'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Ryacas’

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'mockery', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DESeq2', 'ggplot2', 'ggfortify'

Packages suggested but not available for checking:
  'shiny', 'shinyBS', 'shinycssloaders', 'shinyjs', 'shinyWidgets',
  'sortable', 'testthat', 'rmarkdown', 'sva', 'plotly', 'svglite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'Rcpp'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggsci'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'janitor', 'reshape2', 'stringr', 'tidyr', 'dplyr', 'SuperLearner',
  'ggplot2', 'ranger'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DatabionicSwarm’

Packages suggested but not available for checking:
  'plotly', 'geometry', 'FCPS', 'ProjectionBasedClustering',
  'DataVisualizations', 'ggplot2', 'pcaPP', 'spdep', 'igraph', 'cccd',
  'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'kernlab', 'CVST'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'CompQuadForm', 'cowplot', 'ggplot2', 'GiRaF',
  'Rcpp', 'Seurat', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SuperLearner', 'np', 'future.apply'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'nloptr', 'stringi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'dplyr', 'plotly', 'icenReg', 'eventPred', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cubature', 'progressr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr', 'kableExtra', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CDMConnector', 'dplyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'duckdb', 'odbc', 'rmarkdown', 'lubridate', 'DT', 'PaRe',
  'magick', 'DiagrammeRsvg', 'ggplot2', 'cowplot', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'doseminer', 'tidyr', 'sqldf', 'stringr', 'DescTools'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'kableExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'pheatmap', 'ChemmineR', 'rvest', 'tidyr', 'reshape2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CDMConnector', 'dbplyr', 'dplyr', 'lubridate', 'tidyr', 'RJSONIO',
  'PatientProfiles'

Packages suggested but not available for checking:
  'covr', 'testthat', 'odbc', 'RPostgres', 'duckdb',
  'CodelistGenerator', 'PaRe', 'rmarkdown', 'DT', 'magick',
  'DiagrammeRsvg', 'ggplot2', 'cowplot', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GSVA', 'clusterProfiler', 'igraph', 'pheatmap', 'ChemmineR'

Packages suggested but not available for checking: 'rmarkdown', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'unikn'

Packages suggested but not available for checking: 'rmarkdown', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'adaptivetau', 'dplyr', 'ggplot2', 'lhs', 'nloptr', 'plotly'

Packages suggested but not available for checking:
  'covr', 'devtools', 'emoji', 'pkgdown', 'rmarkdown', 'roxygen2',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'adaptivetau', 'dplyr', 'ggplot2', 'lhs', 'nloptr', 'plotly'

Packages suggested but not available for checking:
  'covr', 'devtools', 'emoji', 'pkgdown', 'rmarkdown', 'roxygen2',
  'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'caret', 'kohonen', 'pROC', 'xgboost'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tsoutliers', 'htmlwidgets', 'forecast', 'dygraphs',
  'reshape2', 'seastests'

Packages suggested but not available for checking: 'rmarkdown', 'stR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2', 'cowplot', 'spelling'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Errors in running code in vignettes:
when running code in ‘additional_topics.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘end_to_end_workflow.rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘no_empty_drops.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘understanding_dsb.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : 
  vignette builder 'rmarkdown' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘additional_topics.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘end_to_end_workflow.rmd’ using ‘UTF-8’... failed to complete the test
  ‘no_empty_drops.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘understanding_dsb.Rmd’ using ‘UTF-8’... failed to complete the test
Packages required but not available:
  'dplyr', 'Rcpp', 'stringr', 'tidyr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ggplot2', 'kableExtra', 'lme4', 'patchwork', 'rmarkdown', '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: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'TMB', 'sem', 'igraph', 'RcppEigen'

Packages suggested but not available for checking:
  'AER', 'phylopath', 'rmarkdown', 'reshape', 'dynlm', 'ggplot2',
  'ggpubr', 'ggraph', 'testthat'

Packages which this enhances but not available for checking:
  'rstan', 'tmbstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Documented arguments not in \usage in Rd file 'forecastCovCompiled.Rd':
  ‘obj’ ‘zero’ ‘trend’ ‘estimation.sample’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:

  Warning: 'is.R' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'copula', 'gratia'

Packages suggested but not available for checking: 'plm', 'sfaR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dssd', 'mrds', 'Distance', 'sf', 'ggplot2', 'dplyr'

Packages suggested but not available for checking:
  'testthat', 'lwgeom', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'rmarkdown', 'tidyr', 'ggplot2', 'dplyr', 'testthat', 'wordcloud2',
  'viridis'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ggplot2', 'scales'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'Rcpp', 'stringr'

Packages suggested but not available for checking:
  'covr', 'testthat', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MolgenisAuth', 'stringr', 'urltools'

Packages suggested but not available for checking:
  'dsBaseClient', 'mockery', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mrds', 'ggplot2', 'plyr'

Packages suggested but not available for checking: 'Distance', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘opalr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'ggplot2', 'scales'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'exactci', 'asht'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'lubridate', 'readr', 'stringr', 'tidyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'ggplot2'

Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mcmcse', 'posterior', 'rust', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'cowplot', 'ggplot2', 'gstat', 'interp', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'rtdists', 'ggplot2', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BiasedUrn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'igraph', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'FNN', 'mixtools', 'e1071', 'dplyr', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'pomp', 'Hmisc', 'dplyr', 'r2d3', 'shiny'

Packages suggested but not available for checking:
  'rmarkdown', 'latticeExtra', 'widgetframe', 'tidyr', 'rms'

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'WeightedCluster', 'EnvStats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'pROC', 'caret', 'epiR', 'ggplot2', 'ggpubr', 'glmnet'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
checkRd: (-1) pv.prev.Rd:24: Lost braces; missing escapes or markup?
    24 |   - PPV = 1 / {1 + (1 / pi - 1) / pDLR}
       |               ^
checkRd: (-1) pv.prev.Rd:25: Lost braces; missing escapes or markup?
    25 |   - NPV = 1 / {1 + (1 / (1 / pi - 1)) / nDLR}. 
       |               ^
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) efron.petrosian.Rd:22: Lost braces
    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
checkRd: (-1) lynden.Rd:21: Lost braces
    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
checkRd: (-1) shen.Rd:24: Lost braces
    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'rgl', 'oro.nifti', 'oro.dicom'

Package suggested but not available for checking: ‘covr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
checkRd: (-1) applied_crm.Rd:64: Lost braces; missing escapes or markup?
    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'htmltools', 'stringr', 'tidyr', 'V8', 'fs', 'pdftools'

Packages suggested but not available for checking:
  'rmarkdown', 'devtools', 'testthat', 'ggplot2', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmltools', 'htmlwidgets', 'httpuv', 'crosstalk', 'jquerylib',
  'promises'

Packages suggested but not available for checking:
  'rmarkdown', 'shiny', 'bslib', 'future'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'kernlab', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'fgsea', 'igraph', 'tidyr', 'BiocParallel', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dygraphs', 'RcppCCTZ', 'rmarkdown', 'runner', 'units'
Running ‘tinytest.R’ [2s/3s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("DTSg")
  + }
  
  test_DTSg.R...................    0 tests    
  test_DTSg.R...................    1 tests [0;32mOK[0m 
  test_DTSg.R...................    2 tests [0;32mOK[0m Missing values are always stripped regardless of the value of a possible "na.rm" argument.
  
  test_DTSg.R...................    3 tests [0;32mOK[0m Missing values are always stripped regardless of the value of a possible "na.rm" argument.
  
  test_DTSg.R...................    4 tests [0;32mOK[0m .n column calculated from .dateTime column.
  
  test_DTSg.R...................    5 tests [0;32mOK[0m .n column calculated from .dateTime column.
  
  test_DTSg.R...................    6 tests [0;32mOK[0m 
  test_DTSg.R...................    7 tests [0;32mOK[0m 
  test_DTSg.R...................    8 tests [0;32mOK[0m 
  test_DTSg.R...................    9 tests [0;32mOK[0m 
  test_DTSg.R...................   10 tests [0;32mOK[0m 
  test_DTSg.R...................   11 tests [0;32mOK[0m 
  test_DTSg.R...................   12 tests [0;32mOK[0m 
  test_DTSg.R...................   13 tests [0;32mOK[0m 
  test_DTSg.R...................   14 tests [0;32mOK[0m Error: Package "RcppCCTZ" must be installed for this approach.
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'spelling', 'testthat'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'nanotime', 'Rcpp', 'RcppCCTZ'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘e1071’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'ggrepel', 'RSpectra', 'Rcpp', 'RcppParallel',
  'reshape2', 'shiny', 'shinyjs', 'RcppArmadillo', 'RcppThread'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'e1071', 'DTWBI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ff', 'ggplot2', 'ggrepel'

Packages suggested but not available for checking: 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Objects in \usage without \alias in Rd file 'd.spls.norm1.Rd':
  ‘d.spls.norm2’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'haven', 'readxl', 'readr', 'digest', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'covr', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dbplyr', 'dplyr', 'duckdb'

Packages suggested but not available for checking:
  'sf', 'spelling', 'minioclient', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'adbcdrivermanager', 'arrow', 'DBItest', 'dbplyr', 'dplyr',
  'testthat'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/duckdb.Rcheck/00install.out’ for details.
Package required but not available: ‘crul’

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'duckdb'

Packages suggested but not available for checking:
  'arrow', 'constructive', 'dbplyr', 'lobstr', 'lubridate', 'qs',
  'reprex', 'styler', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'scales'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggmosaic', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'tidyverse', 'ggplot2', 'rstatix'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'stringr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'lintr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggplot2', 'shiny', 'DT', 'reshape2'

Package suggested but not available for checking: ‘bs4Dash’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dplyr', 'cubature', 'ggplot2', 'Rcpp', 'survey', 'tab'

Packages suggested but not available for checking: 'rmarkdown', 'RcppRoll'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'tsDyn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'digest', 'dplyr', 'stringr'

Packages suggested but not available for checking:
  'testthat', 'mockery', 'readr', 'usethis', 'rmarkdown', 'patrick',
  'stringi', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'testthat', 'terra'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'glmnet', 'hglasso'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape', 'Seurat', 'ROCR', 'dplyr', 'e1071', 'MAST'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GenEst', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maxLik', 'Ecdat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcppZiggurat', 'Rfast'

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'htmlwidgets', 'htmltools'

Package suggested but not available for checking: ‘testthat’

Packages which this enhances but not available for checking:
  'rmarkdown', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'readr', 'lubridate', 'imputeTS', 'scales', 'greybox',
  'matlib', 'narray'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/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', 'geosphere', 'terra'

Packages suggested but not available for checking:
  'rmarkdown', 'eesim', 'gstat', 'ggplot2', 'dplyr', 'lubridate',
  'stringr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'ggplot2', 'patchwork', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'googledrive', 'lubridate', 'reticulate', 'rgee', 'terra',
  'tidyr', 'sf', 'readr'

Packages suggested but not available for checking:
  'ape', 'CoordinateCleaner', 'covr', 'gargle', 'gbm', 'ggplot2',
  'magick', 'rmarkdown', 'spThin', 'stars', 'testthat', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'patchwork', 'posterior', 'rstan'

Packages suggested but not available for checking:
  'bookdown', 'cmdstanr', 'covr', 'dplyr', 'rmarkdown', 'testthat',
  'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available:
  'ggplot2', 'viridis', 'scales', 'av', 'ari', 'gganimate'

Packages suggested but not available for checking: 'imager', 'fs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'reshape2', 'dplyr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'raster', 'rmarkdown', 'bookdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'interp', 'tgp', 'plgp'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dynaTree.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘readxl’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'minqa', 'Rcpp'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'Hmisc', 'rmarkdown', 'testthat', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'dynutils', 'lmds'

Packages suggested but not available for checking:
  'testthat', 'diffusionMap', 'igraph', 'lle', 'RANN', 'Rtsne',
  'smacof', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DescTools', 'doRNG', 'ggplot2', 'pec', 'prodlim', 'stringr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'dynutils', 'ggplot2', 'ggraph', 'ggrepel', 'GillespieSSA2',
  'igraph', 'lmds', 'patchwork', 'tidygraph', 'tidyr', 'viridis'

Packages suggested but not available for checking:
  'anndata', 'covr', 'dynwrap', 'R.rsp', 'rmarkdown', 'Seurat',
  'testthat'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking:
  'devtools', 'usethis', 'rmarkdown', 'covr', 'testthat', 'lintr',
  'pkgdown', 'prettydoc', 'pander', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'ggplot2', 'plotly', 'rms', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Produc.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:22: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'carrier', 'dplyr', 'dynutils', 'stringr', 'tidyr'

Packages suggested but not available for checking: 'lhs', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'covr', 'testthat'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'ggplot2', 'reshape2', 'dplyr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MCMCpack’
Packages required but not available:
  'ggplot2', 'latex2exp', 'reshape2', 'plyr', 'mice', 'fda', 'car',
  'stringi'

Packages suggested but not available for checking:
  'testthat', 'roxygen2', 'rmarkdown', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘DataCombine’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'splines2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'kernlab', 'rgenoud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'proxyC', 'Rcpp', 'stringr'

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'babelwhale', 'dplyr', 'dynutils', 'dynparam', 'igraph', 'readr',
  'stringr', 'reshape2', 'tidyr'

Packages suggested but not available for checking:
  'covr', 'dyndimred', 'pkgload', 'ranger', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'BiocParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ggplot2', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/e1071.Rcheck/00install.out’ for details.
Packages required but not available:
  'DataCombine', 'anytime', 'ggplot2', 'scales', 'accelerometry'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'spelling'
GNU make is a SystemRequirements.
Running ‘eafplot.R’ [1s/1s]
  Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shinyFiles', 'shinyBS', 'ggplot2', 'ggthemes', 'plotly', 'shiny',
  'shinythemes', 'shinyjs', 'fontawesome', 'RcppEigen', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hdi', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'DT', 'leaflet', 'plotly', 'shiny', 'shinydashboard',
  'shinyWidgets'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'EpiEstim', 'epitrix', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'vdiffr', 'roxygen2', 'incidence', 'rmarkdown',
  'projections', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'tgp', 'fields', 'som', 'spam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'terra', 'rsconnect', 'testthat', 'sf', 'fs', 'readr',
  'spelling', 'gdalcubes'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
checkRd: (-1) varmod.Rd:99-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) varmod.Rd:102-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) varmod.Rd:105-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) varmod.Rd:109-112: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppThread', 'RcppEigen'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggmap’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'tidyr', 'dplyr', 'ggalluvial', 'ggplot2', 'ggridges', 'recipes',
  'stringr', 'progressr'

Packages suggested but not available for checking:
  'testthat', 'covr', 'vdiffr', 'pkgdown', 'workflows', 'future',
  'furrr', 'e1071', 'caret', 'parsnip', 'vip', 'glmnet', 'xgboost'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BDgraph', 'bgms', 'dplyr', 'ggplot2', 'igraph', 'qgraph'

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', 'tidyr', 'stringr'

Packages suggested but not available for checking: 'posterior', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Packages suggested but not available for checking: 'sf', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
Packages suggested but not available for checking:
  'RMariaDB', 'rmarkdown', 'RPostgres', 'RSQLite', 'testthat'
Packages required but not available: 'rcompanion', 'FSA', 'car'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘PMCMRplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'ggplot2', 'plotly', 'shiny', 'shinycssloaders', 'shinybusy'

Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'qvalue', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘OpenMx’

Package suggested but not available for checking: ‘rpf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ArrayToNc.Rd:30-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:39-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:51-76: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘devtools’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stringr', 'LaF'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available:
  'digest', 'dplyr', 'Hmisc', 'lubridate', 'readxl', 'stringr'

Packages suggested but not available for checking:
  'pdftools', 'qs', 'testthat', 'readxlsb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SSBtools', 'sdcTable', 'shiny'

Packages suggested but not available for checking:
  'rmarkdown', 'RegSDC', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘see’

Packages suggested but not available for checking:
  'DT', 'flexdashboard', 'mockery', 'rmarkdown', 'testthat', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dplyr', 'scales'

Package suggested but not available for checking: ‘randomcoloR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SpecsVerification', 'Rcpp'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'R.rsp', 'verification'

VignetteBuilder packages required for checking but not installed:
  'rmarkdown', 'R.rsp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rglpk’

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown', 'readxl', 'Rsymphony'

Package which this enhances but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSQLite’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'eatDB', 'haven', 'plyr', 'stringi'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'covr', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qcr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'conflicted', 'ggplot2', 'ggparty', 'ggrepel', 'reshape2'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'kableExtra', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'survey', 'BIFIEsurvey', 'Hmisc', 'mice', 'car', 'reshape2', 'plyr',
  'miceadds', 'tidyr', 'EffectLiteR', 'estimatr', 'eatGADS', 'janitor',
  'lme4'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'dplyr', 'ggplot2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fda’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spelling', 'testthat', 'rmarkdown'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘igraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'arrow', 'dplyr', 'sf', 'stringr', 'terra'

Packages suggested but not available for checking:
  'fields', 'ggplot2', 'rmarkdown', 'rnaturalearth', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'plyr', 'separationplot', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'e1071', 'C50', 'pROC', 'smotefamily'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ashr', 'mixsqp', 'dplyr', 'ggplot2'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ROCR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'testthat', 'roxygen2'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'HDF5Array', 'ncmeta', 'reshape2', 'rhdf5', 'stringr',
  'terra', 'tidyterra'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidyr', 'drc'

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'ggridges', 'cowplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dendextend', 'dplyr', 'ggplot2', 'labdsv', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'ggdendro', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Packages required but not available: 'rsdmx', 'xml2'

Packages suggested but not available for checking:
  'rmarkdown', 'dplyr', 'lubridate', 'ggplot2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘digest’

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Ecfun’

Packages suggested but not available for checking: 'plm', 'systemfit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'spatstat.explore', 'spatstat.model',
  'spatstat.random'

Package suggested but not available for checking: ‘dixon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fda', 'stringi', 'xml2', 'BMA', 'rvest'

Packages suggested but not available for checking:
  'car', 'DescTools', 'Ecdat', 'pryr', 'rmarkdown', 'ipumsr',
  'lubridate', 'bayesplot', 'bssm', 'ggplot2', 'kableExtra',
  'openxlsx', 'EnvStats', 'drc', 'prodlim', 'plyr', 'raster', 'readxl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ECGofTestDx.Rcheck/00install.out’ for details.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmlwidgets', 'dplyr', 'broom', 'shiny', 'scales', 'htmltools'

Packages suggested but not available for checking:
  'tidyr', 'testthat', 'rmarkdown', 'covr', 'data.tree', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'htmlwidgets', 'dplyr', 'data.tree'

Packages suggested but not available for checking:
  'htmltools', 'shiny', 'crosstalk', 'testthat', 'sf', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
Argument items with no description in Rd file 'e.cluster.decision.Rd':
  ‘reg_data’ ‘log.lambda’
Argument items with no description in Rd file 'e.cluster.dendrogram.Rd':
  ‘echelon.obj’ ‘n.sim’ ‘cluster.legend.pos’ ‘cluster_reg’ ‘p_rank’
  ‘para’
Argument items with no description in Rd file 'e.cluster.map.Rd':
  ‘x’ ‘c_separates’ ‘locs’ ‘coo’ ‘rin’ ‘p_rank’ ‘cluster_reg’ ‘n.sim’
  ‘cluster.type’
Argument items with no description in Rd file 'e.dendrogram.Rd':
  ‘peaks’ ‘locs’ ‘x’ ‘separates’ ‘c_separates’ ‘number’ ‘parents’
  ‘pare_locs’ ‘progeny’ ‘symbols’ ‘col.symbols’ ‘cex.symbols’ ‘lwd’
  ‘col’ ‘ens’ ‘adj.ens’ ‘col.ens’ ‘cex.ens’ ‘limb’
Argument items with no description in Rd file 'e.dendrogram.axis.Rd':
  ‘main’ ‘ylab’ ‘yaxes’ ‘ylim’ ‘xaxes’ ‘xdper’ ‘dmai’ ‘peaks’ ‘x’
Argument items with no description in Rd file 'e.main.Rd':
  ‘x’ ‘rin’ ‘T’
Argument items with no description in Rd file 'e.monte.bin.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.monte.poi.Rd':
  ‘rin’ ‘cas’ ‘pop’ ‘ex’ ‘n.sim’ ‘K’ ‘cluster.type’
Argument items with no description in Rd file 'e.profile.Rd':
  ‘peaks’ ‘parents’ ‘separates’
Argument items with no description in Rd file 'e.scan.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’
Argument items with no description in Rd file 'e.scan.pop.Rd':
  ‘x’ ‘locs’ ‘peaks’ ‘c_separates’ ‘parents’ ‘K’ ‘pop’
Argument items with no description in Rd file 'nlimb.Rd':
  ‘x’ ‘k2’
Package required but not available: ‘animation’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'ggplot2'
Package required but not available: ‘geosphere’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'Rcpp', 'stringr', 'tidyr', 'RcppArmadillo'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'bayesm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'spelling', 'testthat'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'dplyr', 'plyr', 'readr', 'sf', 'tidyr'

Packages suggested but not available for checking: 'httptest', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'fs', 'geouy', 'haven', 'janitor', 'labelled', 'srvyr',
  'statar', 'stringr', 'survey', 'tidyr'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'furrr', 'future', 'ggplot2', 'patchwork', 'progressr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'caret', 'WGCNA', 'stringr', 'pander'

Packages suggested but not available for checking:
  'rmarkdown', 'factoextra', 'ComplexHeatmap', 'pheatmap', 'viridis',
  'pROC', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘memoise’

Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'testthat', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'ggpubr'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'SSP'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'sf', 'rasterVis', 'ggplot2', 'landscapemetrics',
  'geodata', 'rasterDT'

Packages suggested but not available for checking:
  'rmarkdown', 'xml2', 'rvest', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'EML', 'emld', 'geosphere', 'ggplot2', 'lubridate',
  'neonUtilities', 'rmarkdown', 'stringr', 'tidyr', 'xml2'

Packages suggested but not available for checking:
  'ritis', 'taxize', 'testthat', 'worrms', 'ggrepel', 'usmap', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvabund', 'plyr', 'igraph'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'tidyr', 'ggplot2', 'ggraph', 'labdsv',
  'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'jagsUI', 'ggmcmc'

Packages suggested but not available for checking:
  'rmarkdown', 'devtools', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'dplyr', 'ggplot2',
  'reshape2', 'cowplot', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'picante', 'FD'

Packages suggested but not available for checking:
  'raster', 'alphahull', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seacarb’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  'ape', 'picante', 'rmarkdown', 'testthat', 'untb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'e1071', 'FNN', 'igraph'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggplot2', 'scales'
checkRd: (-1) ecolRxC.Rd:161-166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:167-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:176-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:179-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:186-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:193-201: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:202-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:209-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:217-221: Lost braces in \itemize; meant \describe ?
Running examples in ‘ecolRxC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.ecolRxC
> ### Title: Graphical representation of a RxC ecological inference (vote
> ###   transfer) matrix
> ### Aliases: plot.ecolRxC
> 
> ### ** Examples
> 
> votes1 <- structure(list(P1 = c(16L, 4L, 13L, 6L, 1L, 16L, 6L, 17L, 48L, 14L),
+                          P2 = c(8L, 3L, 0L, 5L, 1L, 4L, 7L, 6L, 28L, 8L),
+                          P3 = c(38L, 11L, 11L, 3L, 13L, 39L, 14L, 34L, 280L, 84L),
+                          P4 = c(66L, 5L, 18L, 39L, 30L, 57L, 35L, 65L, 180L, 78L),
+                          P5 = c(14L, 0L, 5L, 2L, 4L, 21L, 6L, 11L, 54L, 9L),
+                          P6 = c(8L, 2L, 5L, 3L, 0L, 7L, 7L, 11L, 45L, 17L),
+                          P7 = c(7L, 3L, 5L, 2L, 3L, 17L, 7L, 13L, 40L, 8L)),
+                          row.names = c(NA, 10L), class = "data.frame")
> votes2 <- structure(list(C1 = c(2L, 1L, 2L, 2L, 0L, 4L, 0L, 4L, 19L, 14L),
+                          C2 = c(7L, 3L, 1L, 7L, 2L, 5L, 3L, 10L, 21L, 6L),
+                          C3 = c(78L, 7L, 28L, 42L, 28L, 84L, 49L, 85L, 260L, 100L),
+                          C4 = c(56L, 14L, 20L, 7L, 19L, 54L, 22L, 50L, 330L, 91L),
+                          C5 = c(14L, 3L, 6L, 2L, 3L, 14L, 8L, 8L, 45L, 7L)),
+                          row.names = c(NA, 10L), class = "data.frame")
> example <- ecolRxC(votes1, votes2, method = "IPF")
> p <- plot(example, show.plot = FALSE)
Error: Package ggplot2 needed for this function to work. Please install it.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'igraph', 'ggplot2'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'covr', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'intergraph', 'plyr', 'dplyr', 'progressr'

Packages suggested but not available for checking: 'testthat', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'igraph', 'rdiversity', 'blockmodels', 'bipartite', 'Rcpp',
  'RcppEigen', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Packages suggested but not available for checking:
  'testthat', 'ggplot2', 'ggraph', 'rmarkdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'bipartite'

Packages suggested but not available for checking:
  'igraph', 'readr', 'rmarkdown', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvabund', 'ecoCopula'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'ecotraj', 'GDAtools', 'smacof', 'stringr'

Packages suggested but not available for checking:
  'primer', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'covr'
GNU make is a SystemRequirements.
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘FD’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ade4', 'gbm', 'adehabitatHR', 'biomod2', 'dismo', 'ecodist',
  'terra', 'classInt', 'ks', 'nabor', 'Hmisc'

Packages suggested but not available for checking:
  'alphahull', 'dplyr', 'rms', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvabund', 'ecoCopula', 'GET'

Packages suggested but not available for checking:
  'rmarkdown', 'ade4', 'caper', 'car', 'DAAG', 'DHARMa', 'dplyr',
  'GGally', 'ggplot2', 'ggthemes', 'glmnet', 'gllvm', 'glmmTMB',
  'lme4', 'MCMCglmm', 'pgirmess', 'phylobase', 'phylosignal',
  'reshape2', 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'e1071', 'ggplot2', 'qgraph', 'igraph', 'philentropy', 'plyr',
  'reshape', 'Rmisc'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'bookdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'dplyr', 'ggplot2', 'Hmisc', 'openxlsx', 'readr', 'testthat',
  'tidyr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'RSQLite', 'dbplyr', 'dplyr', 'readr', 'readxl', 'rvest', 'stringr',
  'tidyr'

Packages suggested but not available for checking:
  'standartox', 'testthat', 'webchem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'ape', 'rmarkdown', 'smacof', 'ggplot2', 'hrbrthemes', 'reshape2',
  'scales', 'tidyr', 'viridis', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'CVXR', 'multiridge', 'pROC', 'JOPS'

Packages suggested but not available for checking:
  'ggplot2', 'ggraph', 'igraph', 'ggpubr', 'scales', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'smoof', 'Rcpp', 'reshape2', 'ggplot2', 'viridis', 'dplyr',
  'plot3Drgl', 'plotly', 'kableExtra'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'mlr', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WeightSVM’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat', 'caret', 'dplyr', 'e1071', 'kernlab',
  'transport'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future', 'future.apply'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'dae', 'dplyr', 'ggplot2', 'lmerTest', 'predictmeans',
  'supernova'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'spdep', 'sf', 'stringr', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'ggplot2', 'haven', 'labelled', 'readr', 'stringr', 'tidyr'

Packages suggested but not available for checking:
  'janitor', 'plotly', 'testthat', 'vdiffr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bupaR', 'dplyr', 'ggplot2', 'ggthemes', 'shiny', 'miniUI', 'tidyr',
  'shinyTime', 'lubridate', 'stringr'

Packages suggested but not available for checking:
  'rmarkdown', 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) read.edf.Rd:30: Lost braces
    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'ggplot2'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘CompQuadForm’

Packages suggested but not available for checking:
  'rmarkdown', 'stringi', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'tm', 'stringr', 'stringi', 'qdapRegex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xml2’

Packages suggested but not available for checking:
  'covr', 'ggplot2', 'lintr', 'rmarkdown', 'httptest', 'tokenizers',
  'devtools', 'dplyr', 'tidyr', 'roxygen2', 'pkgdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'igraph', 'reticulate', 'interp'

Packages suggested but not available for checking: 'testthat', 'tidygraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'htmlwidgets', 'rjson', 'igraph', 'shiny'

Package suggested but not available for checking: ‘huge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘dae’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'openxlsx2', 'visNetwork', 'blocksdesign'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'dplyr', 'stars'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'reshape2', 'RcppArmadillo'

Package suggested but not available for checking: ‘simcdm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'shiny', 'shinyjs', 'DT', 'dplyr', 'fontawesome'

Packages suggested but not available for checking:
  'testthat', 'dtplyr', 'RSQLite', 'dbplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'miniUI', 'DT', 'dplyr', 'rio', 'shinyWidgets', 'openxlsx'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'OCNet', 'rivnet', 'BayesianTools', 'DHARMa', 'terra',
  'fields'

Packages suggested but not available for checking: 'rmarkdown', 'bookdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘igraph’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xml2’

Packages suggested but not available for checking:
  'readr', 'vcr', 'rmarkdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'stringr'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'lbfgs', 'nloptr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) items_ordered_eclsk_atl.Rd:23: Lost braces; missing escapes or markup?
    23 | \item \code{P4SRS10}: Keep working at something until {he/she} is finished?
       |                                                       ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'energy', 'dHSIC', 'rBayesianOptimization'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'Dire', 'haven', 'LaF', 'lme4', 'readxl', 'wCorr', 'WeMix',
  'xml2'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘broom’

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'readr', 'gstat', 'leaflet', 'raster', 'htmlwidgets', 'dplyr',
  'ggplot2', 'lubridate', 'stringr', 'tidyr', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'rstanarm', 'ggplot2'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'Rlibeemd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'nnfor', 'Rlibeemd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'keras', 'tensorflow', 'reticulate', 'tsutils', 'Rlibeemd',
  'TSdeeplearning'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rlibeemd', 'e1071'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'Rlibeemd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggplot2'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stringr', 'dplyr', 'viridis'

Packages suggested but not available for checking:
  'cdom', 'testthat', 'rmarkdown', 'ggplot2', 'tidyr', 'shiny', 'DT',
  'MBA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'arm'

Packages suggested but not available for checking:
  'testthat', 'stringr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lubridate', 'viridis'

Packages suggested but not available for checking:
  'ggplot2', 'rmarkdown', 'tidyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘PMA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EFAtools', 'mirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'scales', 'ggplot2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'ggplot2', 'dplyr', 'Rcpp', 'future.apply', 'future',
  'tidyr', 'progressr', 'RcppArmadillo'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dplyr', 'ggplot2', 'rmarkdown', 'sf', 'testthat'
Running ‘test_checks.R’ [1s/1s]
  Running ‘test_donothing.R’ [1s/1s]
  Running ‘test_estim.R’ [1s/1s]
  Comparing ‘test_estim.Rout’ to ‘test_estim.Rout.save’ ... OK
  Running ‘test_factor.R’ [1s/1s]
  Running ‘test_factors.R’ [1s/2s]
  Running ‘test_prior_ff.R’ [1s/1s]
  Running ‘test_split.R’ [0s/1s]
  Running ‘test_transprobs.R’ [1s/1s]
Running the tests in ‘tests/test_checks.R’ failed.
Complete output:
  > library(efdm)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/test_donothing.R’ failed.
Complete output:
  > library(efdm)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/test_factor.R’ failed.
Complete output:
  > library(efdm)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/test_split.R’ failed.
Complete output:
  > data.table::setDTthreads(1)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Running the tests in ‘tests/test_transprobs.R’ failed.
Complete output:
  > library(efdm)
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'copula', 'gstat', 'tidyr', 'dplyr'

Packages suggested but not available for checking:
  'rmarkdown', 'ggplot2', 'fields', 'animation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcalg', 'RBGL', 'igraph'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'ggplot2', 'car'

Packages suggested but not available for checking:
  'testthat', 'survey', 'lavaan.survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'seqinr', 'ggplot2', 'shiny', 'reshape2', 'rmarkdown', 'viridis'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'see', 'afex', 'BayesFactor', 'brms', 'car', 'gt', 'lme4',
  'lmerTest', 'parsnip', 'rmarkdown', 'rms', 'rstanarm', 'rstantools',
  'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'survey'

Packages suggested but not available for checking:
  'pbkrtest', 'heplots', 'car', 'alr4', 'robustlmm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘miscTools’

Packages suggested but not available for checking: 'DIFlasso', 'DIFboost'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'TMB', 'dplyr', 'RcppEigen'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'dplyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available: 'pROC', 'ROCR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dendextend', 'future', 'future.apply', 'GGally', 'ggplot2',
  'ggpubr', 'igraph', 'progressr', 'qgraph', 'semPlot'

Package suggested but not available for checking: ‘fungible’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'StanHeaders', 'RcppEigen',
  'RcppParallel'

Packages suggested but not available for checking:
  'eggCountsExtra', 'R.rsp', 'testthat'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'gstat', 'shiny', 'SpatialTools'

Packages suggested but not available for checking: 'rmarkdown', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'tidygraph', 'srvyr', 'tidyr'

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'survey', 'shiny', 'igraph', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EGRET’

Packages suggested but not available for checking:
  'testthat', 'rmarkdown', 'pkgdown', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dataRetrieval', 'fields'

Packages suggested but not available for checking:
  'EGRETci', 'rmarkdown', 'testthat', 'pkgdown', 'dplyr', 'lubridate',
  'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'rmarkdown', 'bookdown'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggplot2', 'dplyr', 'stringr', 'tidyr', 'kableExtra', 'scales',
  'quanteda', 'tm', 'pheatmap', 'igraph', 'tidygraph', 'readr',
  'readxl'

Packages suggested but not available for checking: 'testthat', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking: 'vegdata', 'testthat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘eHOF.Rnw’ using knitr

Quitting from lines 34-43 [prep] (eHOF.Rnw)
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
there is no package called 'vegdata'
--- failed re-building ‘eHOF.Rnw’

SUMMARY: processing the following file failed:
  ‘eHOF.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'lubridate', 'pkdata'

Packages suggested but not available for checking:
  'glmnet', 'logistf', 'medExtractR', 'rmarkdown', 'ggplot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'plotly', 'lubridate', 'viridis', 'scales'

Packages suggested but not available for checking:
  'rmarkdown', 'devtools', 'BiocStyle', 'dbscan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dplyr', 'lubridate'

Packages suggested but not available for checking: 'plotly', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'memoise', 'lubridate', 'readxl'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown', 'dplyr', 'tidyr', 'ggplot2',
  'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GA’

Packages suggested but not available for checking: 'igraph', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ei', 'wru', 'dplyr', 'ggplot2', 'mcmcse', 'overlapping', 'sf',
  'stringr', 'tidyr'

Packages suggested but not available for checking:
  'plyr', 'rmarkdown', 'reshape2', 'RJSONIO', 'testthat', 'tigris'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'tidyr', 'stringr', 'ggplot2', 'ggmap', 'viridis', 'sf'

Packages suggested but not available for checking:
  'rmarkdown', 'roxygen2', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘rmarkdown’

VignetteBuilder package required for checking but not installed: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'igraph', 'shiny'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'testthat', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cubature’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'blme', 'reshape2', 'optimx', 'shiny', 'shinydashboard',
  'shinycssloaders', 'readxl', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'raster'

Packages suggested but not available for checking:
  'testthat', 'covr', 'lwgeom', 'units', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'xgboost', 'DALEX', 'ggrepel', 'ggiraphExtra',
  'iBreakDown', 'tidyr', 'scales'

Packages suggested but not available for checking: 'rmarkdown', 'lightgbm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Packages required but not available:
  'dplyr', 'ggplot2', 'isoband', 'ks', 'mapsf', 'sf'

Packages suggested but not available for checking:
  'ggquiver', 'ggspatial', 'ggthemes', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'dplyr', 'tidyr', 'bsplus', 'dendextend', 'haven',
  'reshape2', 'shinyWidgets', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'covr'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'glmnet', 'SiZer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sparseFLMM’

Packages suggested but not available for checking:
  'covr', 'testthat', 'rmarkdown', 'shapes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bindata', 'geepack', 'wgeesel'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'dplyr', 'haven', 'readr'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'prefio', 'RcppThread', 'testthat'

Packages suggested but not available for checking:
  'covr', 'testthat', 'xml2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘usethis’
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) electData.Rd:16: Lost braces; missing escapes or markup?
    16 | Variables: \code{id}  = {identification number},
       |                         ^
checkRd: (-1) electData.Rd:17: Lost braces; missing escapes or markup?
    17 | \code{state} = {state}, \code{age} = age in years on a shifted scale (current age minus 70),
       |                ^
checkRd: (-1) summary.elect.Rd:25: Lost braces; missing escapes or markup?
    25 |  TRUE for output on start-state totals e_{r.} (for \code{S}>0)
       |                                          ^
Packages required but not available:
  'progressr', 'sf', 'terra', 'future', 'furrr', 'units', 'slippymath',
  'raster'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'stringr', 'ggplot2', 'scales', 'sqldf', 'nhdplusTools'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking: 'melt', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringi’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'covr', 'devtools', 'pkgdown', 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package suggested but not available for checking: ‘rmarkdown’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'devtools', 'dplyr', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'covr', 'testthat'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'wdm', 'Rmpfr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ICSNP', 'doRNG'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘calibrator’
checkRd: (-1) elliptic-package.Rd:92: Lost braces
    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘calibrator’

Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
 chunk 50 (label = bacco_flow) 
Error in p.eqn8.supp(theta = c(0, 1/2), D1 = D1.elliptic, D2 = D2.elliptic,  : 
  could not find function "p.eqn8.supp"

--- failed re-building ‘ellipticpaper.Rnw’

--- re-building ‘residuetheorem.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

--- finished re-building ‘residuetheorem.Rnw’

SUMMARY: processing the following file failed:
  ‘ellipticpaper.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'KernelKnn', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'aniDom', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'pROC'

Packages suggested but not available for checking: 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'EloRating', 'Rcpp', 'RcppParallel', 'rstan', 'rstantools', 'aniDom',
  'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'rmarkdown', 'bookdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/elrm.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'testthat', 'covr', 'rmarkdown'
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'shiny', 'shiny.i18n', 'shinybrowser'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'mediation', 'minfi', 'ggplot2',
  'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DataCombine', 'ggplot2', 'lmerTest', 'sjstats', 'anytime', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'digest', 'dplyr', 'htmltools', 'rmarkdown', 'rvest', 'stringi',
  'stringr', 'tidyr', 'urltools', 'xml2'

Packages suggested but not available for checking:
  'cld2', 'cld3', 'jinjar', 'lintr', 'memoise', 'testthat', 'roxygen2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'glmnet', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'suntools', 'RcppArmadillo'

Packages suggested but not available for checking: 'move', 'sf', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'recipes', 'dplyr', 'keras', 'rsample', 'tensorflow', 'tidyr', 'uwot'

Packages suggested but not available for checking:
  'covr', 'dials', 'ggplot2', 'lme4', 'modeldata', 'rmarkdown',
  'rstanarm', 'testthat', 'xgboost'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'FNN', 'ggplot2', 'igraph', 'Rtsne', 'umap', 'uwot'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optimx', 'HelpersMG'

Packages suggested but not available for checking: 'shiny', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'EMD', 'forecast'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Packages suggested but not available for checking:
  'R2jags', 'SuppDists', 'testthat', 'rgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'openxlsx', 'reshape2', 'stringr', 'HLMdiag', 'readODS',
  'saeRobust', 'spdep'

Packages suggested but not available for checking:
  'testthat', 'R.rsp', 'simFrame', 'sf'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
License stub is invalid DCF.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EMD', 'e1071'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘maxLik’

Packages suggested but not available for checking:
  'rmarkdown', 'miscTools', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggplot2', 'tidyr', 'dplyr', 'gganimate'

Package suggested but not available for checking: ‘xml2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'units', 'raster', 'sf'

Packages suggested but not available for checking:
  'testthat', 'covr', 'lwgeom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) EmiStatR-methods.Rd:86: Lost braces; missing escapes or markup?
    86 | execute {EmiStatR} function
       |         ^
checkRd: (-1) input-class.Rd:136: Lost braces; missing escapes or markup?
   136 |     \item{EmiStatR}{\code{signature(x = "input")}: execute {EmiStatR} function }
       |                                                            ^
Packages required but not available: 'xml2', 'jsonld'

Packages suggested but not available for checking:
  'spelling', 'testthat', 'rmarkdown', 'covr', 'rdflib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xml2', 'digest', 'emld', 'rmarkdown', 'dplyr'

Packages suggested but not available for checking:
  'taxadb', 'testthat', 'covr', 'EML', 'units', 'htmlwidgets', 'shiny',
  'shinyjs', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caTools', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bayesplot', 'brms', 'car', 'ggplot2', 'mediation', 'pbkrtest',
  'lme4', 'lmerTest', 'rmarkdown', 'scales', 'testthat'

Packages which this enhances but not available for checking:
  'CARBayes', 'geepack', 'MCMCglmm', 'MCMCpack', 'mice', 'rstanarm',
  'sommer'
Running examples in ‘emmeans-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: auto.noise
> ### Title: Auto Pollution Filter Noise
> ### Aliases: auto.noise
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # (Based on belief that noise/10 is in decibel units)
> noise.lm <- lm(noise/10 ~ size * type * side, data = auto.noise)
> 
> # Interaction plot of predictions
> emmip(noise.lm, type ~ size | side)
Error in .requireNS("ggplot2", "The 'ggplot' engine requires the 'ggplot2' package be installed.") : 
  The 'ggplot' engine requires the 'ggplot2' package be installed.
Calls: emmip -> emmip.default -> .requireNS -> fail
Execution halted
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'reshape', 'ggplot2', 'scales', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GGally', 'ggplot2'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) macacaModels.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) macacaModels.Rd:10-11: Lost braces in \itemize; meant \describe ?
Running ‘test-all.R’ [0s/0s]
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
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'rmarkdown', 'prettydoc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stringr’

Packages suggested but not available for checking: 'covr', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'testthat', 'spelling', 'covr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'Rcpp'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'Cyclops'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘testthat’
checkRd: (-1) WRegTest.Rd:43: Lost braces
    43 | For ordinary least squares estimator, \code{psifun} should be the identity function psifun <- function(t){t}.
       |                                                                                                          ^
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ROCR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plm', 'dplyr', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) EMSC.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EMSC.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EMSC.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EMSC.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sampleSelection’

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlpack', 'ggplot2', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘rmarkdown’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'stringr', 'shiny', 'RSQLite', 'httpuv', 'dplyr', 'readr', 'tidyr',
  'V8'

Packages suggested but not available for checking:
  'ggplot2', 'testthat', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                              ^
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                                            ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'hawkes', 'ACDm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'digest', 'readr', 'testthat'
Rd files without \alias:
  ‘enc-package.Rd’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available: 'readr', 'rmarkdown'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: '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: 'Rcpp', 'maxLik', 'RcppArmadillo'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘maxLik’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘hopbyhop’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘energy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘CompQuadForm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'terra'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'glmnet', 'reshape', 'robustHD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rmarkdown’
Package required but not available: ‘torch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'raster', 'dismo', 'maxnet', 'dplyr', 'tidyr', 'ggplot2', 'glmnet',
  'rangeModelMetadata'

Packages suggested but not available for checking:
  'rmarkdown', 'testthat', 'spocc', 'rasterVis', 'sf', 'blockCV',
  'devtools', 'latticeExtra', 'ecospat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dismo', 'DT', 'gbm', 'ks', 'maxnet', 'ranger', 'scales', 'sf',
  'shiny', 'terra'

Package suggested but not available for checking: ‘geodata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dismo', 'ggplot2', 'lhs', 'ENMeval', 'spatstat.geom',
  'spatstat.random', 'ggpubr', 'terra', 'raster'

Packages suggested but not available for checking:
  'testthat', 'hypervolume', 'leaflet', 'ecospat', 'ranger', 'caret',
  'CalibratR', 'ape', 'reshape2', 'vip', 'pdp', 'fastshap', 'viridis',
  'rmarkdown', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggplot2', 'reshape2', 'plotly'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'dplyr', 'networkD3', 'htmlwidgets', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rjson', 'ggplot2'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'SuppDists', 'ggplot2', 'rmarkdown'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dendextend', 'ggplot2', 'ggdendro', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'kknn', 'gbm', 'e1071', 'glmnet', 'bartMachine'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Package required but not available: ‘EnsembleBase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘EnsembleBase’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EnsembleBase', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'crch', 'SpecsVerification', 'scoringRules', 'pROC'
Package required but not available: ‘caret’

Packages suggested but not available for checking:
  'e1071', 'ipred', 'rmarkdown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dplyr', 'DECIPHER', 'stringr', 'ggplot2', 'reshape2', 'usethis'

Package suggested but not available for checking: ‘rmarkdown’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'testthat', 'rmarkdown'
Packages required but not available: 'glmnet', 'ggplot2'

Packages suggested but not available for checking:
  'digest', 'ggforce', 'qwraps2', 'R.rsp', 'rmarkdown'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘test-all.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package vignette with \VignetteEngine{} not specifying an engine package:
  ‘ensurer.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
Packages required but not available: 'ape', 'ggplot2', 'ggpubr', 'reshape2'

Packages suggested but not available for checking:
  'ade4', 'pkgdown', 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggplot2', 'ggrepel', 'hrbrthemes', 'tidyverse', '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: 'RANN', 'mixtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) entropy.Dirichlet.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:42: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dplyr', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'drc', 'ggplot2'

Packages suggested but not available for checking: 'rmarkdown', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘testthat’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'stringr', 'testthat'
Running ‘test_envDocument.R’ [1s/1s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages suggested but not available for checking:
  'ape', 'picante', 'gplots'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rdisop', 'BiocParallel', 'animation', 'mixtools', 'igraph'

Packages suggested but not available for checking:
  'testthat', 'xcms', 'MSnbase', 'plotly', 'shiny', 'rmarkdown', 'DT',
  'crosstalk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'concaveman', 'cvAUC', 'doFuture', 'doRNG', 'fields', 'future',
  'ROCR', 'sf', 'sparr', 'spatstat.geom', 'terra'

Packages suggested but not available for checking:
  'R.rsp', 'RStoolbox', 'spatstat.random', 'spelling', 'testthat'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kSamples’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kSamples’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rmarkdown', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Packages required but not available:
  'ape', 'bio3d', 'phangorn', 'philentropy', 'seqinr', 'stringr'

Package suggested but not available for checking: ‘testthat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'ecp'

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: 'covr', 'testthat'
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: 'covr', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fs', 'lubridate'

Packages suggested but not available for checking:
  'ipaddress', 'spelling', 'testthat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.