Package required but not available: ‘Rcpp’

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

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

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

Packages suggested but not available for checking:
  'bruceR', 'PsychWordVec', 'text', 'sweater'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'mlr3verse', 'ranger', 'tidymodels'
Running examples in ‘fmeffects-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AverageMarginalEffects
> ### Title: R6 Class computing Average Marginal Effects (AME) based on
> ###   Forward Marginal Effects (FME) for a model
> ### Aliases: AverageMarginalEffects
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `AverageMarginalEffects$new`
> ## ------------------------------------------------
> 
> # Train a model:
> 
> library(mlr3verse)
Error in library(mlr3verse) : there is no package called ‘mlr3verse’
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > 
  > test_check("fmeffects")
  Loading required package: fmeffects
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-compute_ame.R:2:1'): (code run outside of `test_that()`) ───────
  <packageNotFoundError/error/condition>
  Error in `library(mlr3verse)`: there is no package called 'mlr3verse'
  Backtrace:
      ▆
   1. └─base::library(mlr3verse) at test-compute_ame.R:2:1
  ── Error ('test-compute_fme.R:3:3'): FME computation correct ───────────────────
  <packageNotFoundError/error/condition>
  Error in `library(mlr3verse)`: there is no package called 'mlr3verse'
  Backtrace:
      ▆
   1. └─base::library(mlr3verse) at test-compute_fme.R:3:3
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fme_theory.Rmd’ using rmarkdown
--- finished re-building ‘fme_theory.Rmd’

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

Quitting from lines 40-45 [unnamed-chunk-2] (fmeffects.Rmd)
Error: processing vignette 'fmeffects.Rmd' failed with diagnostics:
there is no package called 'mlr3verse'
--- failed re-building ‘fmeffects.Rmd’

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

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

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

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

Packages suggested but not available for checking:
  'inlabru', 'terra', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'caret', 'solitude', 'C50', 'FactoMineR', 'factoextra',
  'RcppArmadillo'

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
checkRd: (-1) FMP.Rd:30: Lost braces; missing escapes or markup?
    30 | \eqn{m(\theta) = b_0 + b_1 \theta + b_2 \theta^2 + b_3 \theta^3}. Acceptable values of k = {0,1,2,3}. According to 
       |                                                                                            ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape’

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

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

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

Packages suggested but not available for checking:
  'ciftiTools', 'RNifti', 'oro.nifti'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ciftiTools', 'RNifti', 'oro.nifti', 'gsignal', 'fda'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘Epi’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) Estable.Rd:40: Lost braces
    40 |   \code{dEstable}{ gives the density function;}
       |                  ^
checkRd: (-1) Estable.Rd:41: Lost braces
    41 |   \code{pEstable}{ gives the distribution function or its complement;}
       |                  ^
checkRd: (-1) Estable.Rd:42: Lost braces
    42 |   \code{qEstable}{ gives quantiles;}
       |                  ^
checkRd: (-1) Estable.Rd:43-56: Lost braces
    43 |   \code{tailsEstable}{ returns a list with the following components
       |                      ^
checkRd: (-1) FMstable.Rd:50: Lost braces
    50 |   \code{dFMstable}{ gives the density function;}
       |                   ^
checkRd: (-1) FMstable.Rd:51: Lost braces
    51 |   \code{pFMstable}{ gives the distribution function or its complement;}
       |                   ^
checkRd: (-1) FMstable.Rd:52: Lost braces
    52 |   \code{qFMstable}{ gives quantiles;}
       |                   ^
checkRd: (-1) FMstable.Rd:53-66: Lost braces
    53 |   \code{tailsFMstable}{  returns a list with the following components
       |                       ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘libr’

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 required but not available: ‘TukeyGH77’

Package suggested but not available for checking: ‘mixtools’

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

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

Package suggested but not available for checking: ‘quarto’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggraph', 'minerva'

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

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

Quitting from lines 21-25 [load] (footprint.Rmd)
Error: processing vignette 'footprint.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘footprint.Rmd’

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

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

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

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

Package suggested but not available for checking: ‘psd’

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

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.forecast_model_hyper
> ### Title: Plot hyperparameters
> ### Aliases: plot.forecast_model_hyper
> 
> ### ** Examples
> 
> # Sampled Seatbelts data from the R package datasets.
> data("data_seatbelts", package = "forecastML")
> 
> # Example - Training data for 2 horizon-specific models w/ common lags per predictor.
> horizons <- c(1, 12)
> lookback <- 1:15
> 
> data_train <- create_lagged_df(data_seatbelts, type = "train", outcome_col = 1,
+                                lookback = lookback, horizon = horizons)
> 
> # One custom validation window at the end of the dataset.
> windows <- create_windows(data_train, window_start = 181, window_stop = 192)
> 
> # User-define model - LASSO
> # A user-defined wrapper function for model training that takes the following
> # arguments: (1) a horizon-specific data.frame made with create_lagged_df(..., type = "train")
> # (e.g., my_lagged_df$horizon_h) and, optionally, (2) any number of additional named arguments
> # which are passed as '...' in train_model().
> library(glmnet)
Error in library(glmnet) : there is no package called ‘glmnet’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘combine_forecasts.Rmd’ using rmarkdown

Quitting from lines 40-47 [unnamed-chunk-2] (combine_forecasts.Rmd)
Error: processing vignette 'combine_forecasts.Rmd' failed with diagnostics:
there is no package called 'glmnet'
--- failed re-building ‘combine_forecasts.Rmd’

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

Quitting from lines 30-42 [unnamed-chunk-2] (custom_functions.Rmd)
Error: processing vignette 'custom_functions.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘custom_functions.Rmd’

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

Quitting from lines 82-91 [unnamed-chunk-2] (grouped_forecast.Rmd)
Error: processing vignette 'grouped_forecast.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘grouped_forecast.Rmd’

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

Quitting from lines 29-37 [unnamed-chunk-2] (lagged_features.Rmd)
Error: processing vignette 'lagged_features.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘lagged_features.Rmd’

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

Quitting from lines 150-169 [unnamed-chunk-3] (package_overview.Rmd)
Error: processing vignette 'package_overview.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘package_overview.Rmd’

SUMMARY: processing the following files failed:
  ‘combine_forecasts.Rmd’ ‘custom_functions.Rmd’ ‘grouped_forecast.Rmd’
  ‘lagged_features.Rmd’ ‘package_overview.Rmd’

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

Package suggested but not available for checking: ‘forecTheta’

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:
  'decomposedPSF', 'imputeTestbench', 'reshape2', 'forecast'

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

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

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plotly’

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

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

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

Package suggested but not available for checking: ‘ranger’

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

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

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

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

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

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: ‘gridtext’
Packages suggested but not available for checking: 'Gmisc', 'Greg'
Running ‘forestplot2_vtests.R’ [3s/4s]
  Running ‘test_visual_w_cochrane_mdata.R’ [1s/1s]
  Running ‘test_visual_with_Greg.R’ [0s/0s]
  Running ‘testthat.R’ [3s/4s]
  Running ‘vtest_from_vignette.R’ [2s/2s]
Running the tests in ‘tests/test_visual_with_Greg.R’ failed.
Complete output:
  > library(Greg)
  Error in library(Greg) : there is no package called 'Greg'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rapportools’

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:
  'terra', 'sf', 'imager', 'GLCMTextures'

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

Package suggested but not available for checking: ‘raster’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Packages suggested but not available for checking: 'DT', 'shiny'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(formattable)
  > 
  > test_check("formattable")
  Failed with error:  'there is no package called 'DT''
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 273 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-render.R:9:3'): shiny ──────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'shiny'
  Backtrace:
      ▆
   1. ├─testthat::expect_is(...) at test-render.R:9:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─formattable::renderFormattable(formattable(head(mtcars)))
   5. │ └─htmlwidgets::shinyRenderWidget(...)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base (local) withOneRestart(expr, restarts[[1L]])
   9.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-render.R:18:3'): as.datatable ──────────────────────────────────
  Error in `as.datatable.formattable(f)`: requireNamespace("DT") is not TRUE
  Backtrace:
      ▆
   1. ├─formattable::as.datatable(f) at test-render.R:18:3
   2. └─formattable:::as.datatable.formattable(f)
   3.   └─base::stopifnot(is.formattable(x), requireNamespace("DT"))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 273 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘formattable-data-frame.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'DT''

Quitting from lines 172-173 [unnamed-chunk-19] (formattable-data-frame.Rmd)
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
requireNamespace("DT") is not TRUE
--- failed re-building ‘formattable-data-frame.Rmd’

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

SUMMARY: processing the following file failed:
  ‘formattable-data-frame.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gt’
Packages required but not available:
  'ggforce', 'onbrand', 'shiny', 'shinyAce', 'shinyWidgets'

Packages suggested but not available for checking:
  'devtools', 'DT', 'flextable', 'ggpubr', 'plotly', 'prompter',
  'shinybusy', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘meta’
Packages suggested but not available for checking:
  'ggrepel', 'ibdsim2', 'plotly'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'dbscan', 'lidR', 'plotly', 'raster', 'Rcpp', 'RCSF', 'reticulate',
  'sf', 'VoxR', 'RcppEigen'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'FactoMineR', 'likert'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown

Quitting from lines 25-33 [unnamed-chunk-1] (Overview.Rmd)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘Overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ape', 'ggtree', 'tidytree'

Packages suggested but not available for checking:
  'paleotree', 'devtools', 'TreeSim', 'treeio', 'ggrepel'

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

Package suggested but not available for checking: ‘spelling’

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.
checkRd: (-1) FGf.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FGf.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FourgameteP.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FourgameteP.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘spelling’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gamm4’

Package suggested but not available for checking: ‘refund’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kmeansCBI
> ### Title: Interface functions for clustering methods
> ### Aliases: kmeansCBI hclustCBI hclusttreeCBI disthclustCBI
> ###   disthclusttreeCBI noisemclustCBI distnoisemclustCBI claraCBI pamkCBI
> ###   dbscanCBI mahalCBI mergenormCBI speccCBI tclustCBI pdfclustCBI
> ###   emskewCBI stupidkcentroidsCBI stupidknnCBI stupidkfnCBI
> ###   stupidkavenCBI
> ### Keywords: cluster multivariate
> 
> ### ** Examples
> 
>   options(digits=3)
>   set.seed(20000)
>   face <- rFace(50,dMoNo=2,dNoEy=0,p=2)
>   dbs <- dbscanCBI(face,eps=1.5,MinPts=4)
>   dhc <- disthclustCBI(dist(face),method="average",k=1.5,noisecut=2)
>   table(dbs$partition,dhc$partition)
   
     1
  1 16
  2  9
  3  9
  4  5
  5 11
>   dm <- mergenormCBI(face,G=10,modelNames="EEE",nnk=2)
>   dtc <- tclustCBI(face,6,trim=0.1,restr.fact=500)
Warning in tclustCBI(face, 6, trim = 0.1, restr.fact = 500) :
  tclust could not be loaded
>   table(dm$partition,dtc$partition)
Error in dtc$partition : $ operator is invalid for atomic vectors
Calls: table
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'klaR', 'GGally'

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

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

Packages suggested but not available for checking: 'fixest', 'pdftools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |     ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                        ^
checkRd: (-1) Fpop.Rd:8: Lost braces; missing escapes or markup?
     8 | sum_{i=1}^n (x_i-m_i)^2 + lambda * sum_{i=1}^{n-1} I(m_i !=
       |                                              ^
checkRd: (-1) Fpop.Rd:9: Lost braces; missing escapes or markup?
     9 | m_{i+1}), where the indicator function I counts the number of
       |   ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fAssets', 'fCopulae'

Package suggested but not available for checking: ‘bcp’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fable', 'fabletools', 'feasts', 'tsibble', 'tsibbledata'

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FracKrig
> ### Title: FracKrig
> ### Aliases: FracKrig
> 
> ### ** Examples
> 
> 
> library(sp)
> library(gstat)
Error in library(gstat) : there is no package called ‘gstat’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘RandomFields’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'imager', 'plyr'

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

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

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

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

Package suggested but not available for checking: ‘plotly’

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

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: 'reshape2', 'Rcpp'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) summary.frbs.Rd:32: Lost braces
    32 |                           \code{"GAUSSIAN"}, code{"TRIANGLE"}, \code{"TRAPEZOID"}, \code{"SIGMOID"}, and \code{"BELL"}.
       |                                                  ^
checkRd: (-1) summary.frbs.Rd:60: Lost braces; missing escapes or markup?
    60 |          {4.0, 0.23, 0.43, 0.53, 0.73} on its column. It means that the label a.2 of variable v.1 
       |          ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fdadensity', 'fdapace', 'osqp'

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

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

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

Package suggested but not available for checking: ‘permutations’

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: ‘smacof’

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

Packages suggested but not available for checking:
  'oro.nifti', 'pander', 'fslr'

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

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

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

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: 'reshape2', 'shiny'

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

Package suggested but not available for checking: ‘shiny’

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

Packages suggested but not available for checking:
  'glmnet', 'epiR', 'DescTools', 'survminer', 'BeSS', 'Rfast'

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

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

Packages suggested but not available for checking:
  'shinyWidgets', 'shinydashboard', 'bs4Dash'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'reshape'
Packages suggested but not available for checking: 'devtools', 'reshape'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'fmesher', 'plyr', 'Rcpp', 'sparseinv', 'TMB', 'ggpubr', 'reshape2',
  'RcppEigen'

Packages suggested but not available for checking:
  'dggrids', 'gstat', 'lme4', 'sf', 'spdep', 'verification'

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: 'micEcon', 'plm'

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: 'cna', 'Rfast'

Package suggested but not available for checking: ‘spelling’

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

Packages suggested but not available for checking:
  'DescTools', 'fishmethods', 'marked', 'plyr'

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

Package suggested but not available for checking: ‘Rvcg’

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

Packages suggested but not available for checking:
  'arm', 'Boruta', 'C50', 'car', 'Cubist', 'extraTrees', 'foba',
  'glmnet', 'HDclassif', 'ipred', 'klaR', 'kohonen', 'nodeHarvest',
  'obliqueRF', 'penalized', 'penalizedLDA', 'pROC', 'relaxo', 'rrlda',
  'RSNNS'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) FSelector-package.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FSelector-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) relief.Rd:22: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'RcppArmadillo', 'RTCGA.rnaseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) report.Rd:18: Lost braces; missing escapes or markup?
    18 |         \item{las}{numeric in {0,1,2,3}; the style of axis labels (see \code{\link{par}}).}
       |                               ^
Package required but not available: ‘Rcpp’

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

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

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

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

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

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: 'Rcpp', 'glmnet', 'qpdf', 'RcppEigen'

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

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

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

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

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

Package suggested but not available for checking: ‘nanotime’

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

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

Package suggested but not available for checking: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'forecast', 'rainbow', 'sde', 'fda', 'pdfCluster', 'ecp', 'fdapace',
  'evgam', 'ROOPSD'

Packages suggested but not available for checking: 'fds', 'meboot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'sf', 'units'

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

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

Quitting from lines 55-56 [unnamed-chunk-3] (fullrankmat-comparison.Rmd)
Error: processing vignette 'fullrankmat-comparison.Rmd' failed with diagnostics:
there is no package called 'caret'
--- failed re-building ‘fullrankmat-comparison.Rmd’

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

SUMMARY: processing the following file failed:
  ‘fullrankmat-comparison.Rmd’

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

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

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

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

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

Packages suggested but not available for checking:
  'Ckmeans.1d.dp', 'DescTools', 'DiffXTables', 'GridOnClusters'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'keras', 'tensorflow', 'fda.usc', 'fda', 'ggpubr', 'caret',
  'reshape2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘fields’

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

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

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

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

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

Package suggested but not available for checking: ‘pROC’

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

Package suggested but not available for checking: ‘magick’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ade4', 'tidytext'
Running examples in ‘funrar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distinctiveness
> ### Title: Functional Distinctiveness on site-species matrix
> ### Aliases: distinctiveness
> 
> ### ** Examples
> 
> data("aravo", package = "ade4")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘ade4’
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘funrar.Rmd’ using rmarkdown

Quitting from lines 37-40 [unnamed-chunk-1] (funrar.Rmd)
Error: processing vignette 'funrar.Rmd' failed with diagnostics:
there is no package called 'ade4'
--- failed re-building ‘funrar.Rmd’

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

Quitting from lines 149-172 [aravo_new_distinct] (new_distinctiveness.Rmd)
Error: processing vignette 'new_distinctiveness.Rmd' failed with diagnostics:
there is no package called 'ade4'
--- failed re-building ‘new_distinctiveness.Rmd’

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

Quitting from lines 30-36 [load-data] (other_functions.Rmd)
Error: processing vignette 'other_functions.Rmd' failed with diagnostics:
there is no package called 'ade4'
--- failed re-building ‘other_functions.Rmd’

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

SUMMARY: processing the following files failed:
  ‘funrar.Rmd’ ‘new_distinctiveness.Rmd’ ‘other_functions.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ade4', 'ape', 'ks', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘blogdown’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dbscan', 'mlVAR'

Packages suggested but not available for checking:
  'Ecdat', 'randomcoloR', 'reshape2'

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

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:
  'Rcpp', 'glmnet', 'RSpectra', 'RcppEigen'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘dbscan’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                             ^
checkRd: (-1) trapezoidalApproximation-methods.Rd:49: Lost braces; missing escapes or markup?
    49 | For example, if Val(A) < EV_{1/3}(A) or Val(A) > EV_{2/3}(A),
       |                                                     ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ecp’

Package suggested but not available for checking: ‘spelling’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘markovchain’
Skipping checking math rendering: package 'V8' unavailable
Found the following HTML validation problems:
FuzzyNumberList.html:76:1 (FuzzyNumberList.Rd:285): Warning: trimming empty <ul>
TrapezoidalFuzzyNumberList.html:118:1 (TrapezoidalFuzzyNumberList.Rd:572): Warning: trimming empty <ul>
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: ‘reticulate’

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

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

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.
Package required but not available: ‘Rcpp’

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: 'geosphere', 'JOPS'

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

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

Package suggested but not available for checking: ‘FactoMineR’

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

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

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: ‘GA’

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

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.
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Package suggested but not available for checking: ‘gt’

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

Packages suggested but not available for checking: 'gamm4', 'PLmixed'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘BayesX’
checkRd: (-1) stabsel.mboostLSS.Rd:44: Lost braces
    44 |     always use code{"none"}.}
       |                    ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘gamboostLSS_Tutorial.Rnw’ using Sweave
Loading required package: R2BayesX
Loading required package: BayesXsrc
Loading required package: colorspace
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.
Loading required package: gamboostLSS
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs

Attaching package: 'gamboostLSS'

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

    model.weights

Loading required namespace: BayesX
Failed with error:  'there is no package called 'BayesX''

Error: processing vignette 'gamboostLSS_Tutorial.Rnw' failed with diagnostics:
 chunk 18 (label = run_modeling) 
Error in bmrf(mcdist, bnd = neighborhood) : cannot load 'BayesX'

--- failed re-building 'gamboostLSS_Tutorial.Rnw'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) naref.Rd:13: Lost braces
    13 | \details{ For every \code{factor} or \code{character} column in \code{x}, \code{naref} sets \code{NA} as the reference level for a \code{factor} variable. Columns coded as \code{character} class are first converted to factors via \R{factor(x)}.  If \code{impute=TRUE} then the numeric columns are converted to two columns, one appended \code{.x} that contains imputed values and another appended \code{.miss} which is a binary variable indicating whether the original value was missing.  Numeric columns are returned without change if \code{impute=FALSE} or if they do not contain any missing values.  
       |                                                                                                                                                                                                                                         ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
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Package required but not available: ‘glmnet’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) term.plotZadj.Rd:6: Lost braces
     6 |  \ This is a wrapper to function \code{\link[gamlss]{term.plot}}. code{term.plotZadj} produces term plots for a specified parameter from a    
       |                                                                       ^
Package required but not available: ‘glmnet’

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

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

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

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

Package suggested but not available for checking: ‘Ecdat’

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', 'tensorflow'

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

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

Package suggested but not available for checking: ‘spelling’

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

Package suggested but not available for checking: ‘spam’

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

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

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

Packages suggested but not available for checking:
  'BradleyTerry2', 'DOT', 'MCMCglmm', 'manhattanly', 'meta',
  'pedigree', 'pedigreemm', 'reshape', 'valr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) glag.Rd:7: Lost braces; missing escapes or markup?
     7 | Similar to the \code{\link{lag}} function from the \code{stats} package, but \code{glag} enables padding (e.g. {NA}s or 0s) of the lost entries. Contrary to the \code{\link{lag}} function in the stats package, however, the default in \code{glag} is to pad (with \code{NA}s). The \code{glag} is particularly suited for \code{\link{zoo}} objects, since their indexing is retained
       |                                                                                                                ^
Package required but not available: ‘vcfR’

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

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.
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                      ^
checkRd: (-1) read.ctable.Rd:19: Lost braces; missing escapes or markup?
    19 | a integer scalar which is the index ({icol,irow}) of {row,col}-header
       |                                                      ^
checkRd: (-1) read.ctable.Rd:29: Lost braces; missing escapes or markup?
    29 | output array, {row,col}.names are not necessary \code{dimnames[[1]]} and
       |               ^
Packages required but not available: 'jsonify', 'tidyxl', 'units'

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

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

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

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

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

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

Package suggested but not available for checking: ‘rstantools’

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

Package suggested but not available for checking: ‘RcppEigen’

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ridigbio', 'rgbif', 'CoordinateCleaner', 'terra', 'spThin',
  'leaflet'

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

Packages suggested but not available for checking:
  'ContourFunctions', 'ggrepel', 'lhs', 'splitfngr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) Sim.Markov.Chain.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{eta0}{inital value in {1,...,r}.}
       |                             ^
Package required but not available: ‘metR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GB2’

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

Package suggested but not available for checking: ‘simFrame’

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

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

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', 'SKAT'

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

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'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
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Package suggested but not available for checking: ‘pander’

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: ‘gputools’

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

Package suggested but not available for checking: ‘paleofire’

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

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'

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) listInverseBlocks.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                           ^
checkRd: (-1) listInverseBlocks.Rd:17: Lost braces; missing escapes or markup?
    17 | List all the inverse matrices of the leading sub-matrix of P=Sigma^{-1}
       |                                                                    ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gconsensus.Rd:48-54: Lost braces
    48 | {\code{display.signif.digits} an integer representing the number of significant digits to be obtained in the adaptative approach of the Monte Carlo simulation,
       | ^
Packages required but not available: 'postpack', 'Rcpp', 'RcppArmadillo'

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

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

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

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

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

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

Package suggested but not available for checking: ‘gt’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'FactoMineR', 'ggrepel'

Packages suggested but not available for checking:
  'sf', 'shiny', 'miniUI', 'esquisse', 'rclipboard', 'factoextra',
  'ade4'

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:
  'leaflet', 'shiny', 'DT', 'shinyWidgets', 'shinycssloaders'

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eigcv
> ### Title: Compute cross-validate eigenvalues
> ### Aliases: eigcv
> 
> ### ** Examples
> 
> 
> library(fastRG)
Error in library(fastRG) : there is no package called ‘fastRG’
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(gdim)
  Loading required package: Matrix
  > 
  > test_check("gdim")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-eigcv.R:1:1'): (code run outside of `test_that()`) ─────────────
  <packageNotFoundError/error/condition>
  Error in `library(fastRG)`: there is no package called 'fastRG'
  Backtrace:
      ▆
   1. └─base::library(fastRG) at test-eigcv.R:1:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
Packages required but not available:
  'Rcpp', 'shiny', 'shinydashboard', 'RcppArmadillo'

Packages suggested but not available for checking: 'CDM', 'cdmTools'

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

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

Package suggested but not available for checking: ‘terra’

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

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

Package suggested but not available for checking: ‘gdverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GDSARM.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDSARM.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) GDS_givencols.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) GDS_givencols.Rd:10: Lost braces
    10 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
checkRd: (-1) dantzig.delta.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dantzigS.Rd:7: Lost braces
     7 | Cand{\`e}s, E. and Tao, T. (2007). The Dantzig selector: Statistical estimation when p is much
       |     ^
checkRd: (-1) dataCompoundExt.Rd:6: Lost braces
     6 | \title{Compound Extraction experiment of Dopico-Garc{\' i}a et al. (2007)}
       |                                                     ^
checkRd: (-1) dataCompoundExt.Rd:35: Lost braces
    35 | An analytical experiment conducted by Dopico-Garc{\' i}a et al. (2007) to
       |                                                  ^
checkRd: (-1) dataCompoundExt.Rd:22: Lost braces
    22 | Dopico-Garc{\' i}a, M.S., Valentao, P., Guerra, L., Andrade, P. B., and Seabra, R. M. (2007).
       |            ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘gfonts’

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

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

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

Packages suggested but not available for checking: 'sf', 'gstat', 'spam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'terra', 'geosphere', 'red', 'biomod2'

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

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: 'lme4', 'MESS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) dental.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dental.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seizure.Rd:21: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

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

Packages suggested but not available for checking:
  'inferference', 'AER', 'ICSNP'

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

Package suggested but not available for checking: ‘TreeSim’

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: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) gelnet.logreg.obj.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{y}{n-by-1 binary response vector sampled from {0,1}}
       |                                                     ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

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

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

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: ‘magick’

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:
  'ape', 'ggnetwork', 'ggraph', 'phangorn', 'reshape2', 'shiny',
  'ggtree', 'ShortRead'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘genderdata’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) GeneF-internal.Rd:40: Lost braces; missing escapes or markup?
    40 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
checkRd: (-1) flexorhtest.pvalue.Rd:57: Lost braces; missing escapes or markup?
    57 | \author{Yinglei Lai {ylai@gwu.edu}}
       |                     ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ape', 'ggpubr', 'pegas', 'reshape2', 'shiny', 'shinyjs', 'sf',
  'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clusterProfiler', 'europepmc', 'fst', 'geneset', 'ggraph',
  'openxlsx'

Packages suggested but not available for checking:
  'fgsea', 'ggrepel', 'GOSemSim', 'tm', 'treemap', 'reshape2', 'rrvgo',
  'wordcloud'

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

Package suggested but not available for checking: ‘fgsea’

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

Package suggested but not available for checking: ‘shiny’

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

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

Packages suggested but not available for checking:
  'DataVisualizations', 'reshape2', 'fields', 'plotly'

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

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: 'glmnet', 'ranger'
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
Packages required but not available: 'reshape2', 'reticulate', 'tmod'

Packages suggested but not available for checking:
  'clusterProfiler', 'UpSetR'

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

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

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

Package suggested but not available for checking: ‘shiny’

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

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'learnr', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) LD.Rd:37-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:47-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:66-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:82-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:48-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:59-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:78-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:97-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'exactextractr', 'terra', 'sf', 'sfnetworks', 'spdep'

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

Package suggested but not available for checking: ‘mlpack’

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

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

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

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

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

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

Package suggested but not available for checking: ‘junctions’

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.
Packages required but not available: 'kaos', 'seqinr'

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘SKAT’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘bestglm’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: varhat
> ### Title: Asymptotic variance (times 'n') of the estimator for 'mu' or
> ###   'sigmasq' for the univariate normal on a general domain assuming the
> ###   other parameter is known.
> ### Aliases: varhat
> 
> ### ** Examples
> 
> varhat(0, 1, "min_log_pow", 1, 1, TRUE, make_domain("R+", 1))
Error in varhat(0, 1, "min_log_pow", 1, 1, TRUE, make_domain("R+", 1)) : 
  Please install package "cubature".
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'mvmesh', 'geometry', 'SphericalCubature'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                ^
checkRd: (-1) gensvm.grid.Rd:125: Lost braces
   125 | "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                    ^
checkRd: (-1) gensvm.grid.Rd:127: Lost braces
   127 | GenSVM" in the code{ink{gensvm-package}} page for more info.}
       |                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                        ^
checkRd: (-1) gensvm.grid.Rd:129: Lost braces
   129 | section "Kernels in GenSVM" in the code{ink{gensvm-package}} page for more 
       |                                            ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

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

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

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

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

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

Packages suggested but not available for checking: 'elevatr', 'geosphere'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tmap', 'spdep', 'reldist', 'fclust', 'reshape2', 'shiny', 'sf',
  'leaflet', 'plotly', 'terra', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'ppclust', 'ClustGeo', 'car', 'ggpubr', 'shinyWidgets',
  'shinyhelper', 'waiter'

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

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

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

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

Package suggested but not available for checking: ‘pander’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) calvaria.Rd:8: Lost braces; missing escapes or markup?
     8 | A named list containing \code{x} {a vector containing the ages}
       |                                  ^
checkRd: (-1) calvaria.Rd:9: Lost braces; missing escapes or markup?
     9 |   \code{y} {a matrix where each column is a preshape.} The 23rd, 101st,
       |            ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fields’

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

Package suggested but not available for checking: ‘sf’

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

Packages suggested but not available for checking:
  'ggrepel', 'geofacet', 'leaflet', 'sotkanet'

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

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

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

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gis_tools
> ### Title: Helpers for interfacing geohashes with sp/sf objects
> ### Aliases: gh_to_sp gh_to_spdf gh_to_spdf.default gh_to_spdf.data.frame
> ###   gh_to_sf gh_covering
> 
> ### ** Examples
> 
>   # get the neighborhood of this geohash in downtown Apia as an sp object
>   downtown = '2jtc5x'
>   apia_nbhd = unlist(gh_neighbors(downtown))
>   apia_sp = gh_to_sp(apia_nbhd)
> 
>   # all geohashes covering a random sampling within Apia:
>   apia_covering = gh_covering(smp <- sp::spsample(apia_sp, 10L, 'random'))
Error in check_suggested("sf") : 
  This function requires an installation of sf; install.packages('sf') to proceed.
Calls: gh_covering ... <Anonymous> -> .class1 -> gh_to_sf -> check_suggested
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(geohashTools)
  > 
  > # TODO(#40): activate this
  > # options(warn = 2L)
  > test_check('geohashTools')
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 94 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • sf cannot be loaded (2): 'test-gis-tools.R:116:3', 'test-gis-tools.R:189:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-gis-tools.R:152:3'): gh_covering works ─────────────────────────
  Error in `check_suggested("sf")`: This function requires an installation of sf; install.packages('sf') to proceed.
  Backtrace:
      ▆
   1. └─geohashTools::gh_covering(banjarmasin) at test-gis-tools.R:152:3
   2.   ├─methods::as(gh_to_sf(gh), "Spatial")
   3.   │ └─methods:::.class1(object)
   4.   └─geohashTools::gh_to_sf(gh)
   5.     └─geohashTools:::check_suggested("sf")
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 94 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘geohashTools.Rmd’ using rmarkdown

Quitting from lines 111-121 [merlion_nbhd] (geohashTools.Rmd)
Error: processing vignette 'geohashTools.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘geohashTools.Rmd’

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

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

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

Packages suggested but not available for checking:
  'leaflet', 'leaflet.extras'

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

Packages suggested but not available for checking: 'gistr', 'leaflet'

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

Package suggested but not available for checking: ‘sf’

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

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

Package suggested but not available for checking: ‘jsonify’

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

Packages suggested but not available for checking:
  'redist', 'RcppSimdJson', 'spelling'

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

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

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

Package suggested but not available for checking: ‘geomarocdata’

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:
  'spdep', 'raster', 'terra', 'sf', 'geosphere'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ISOImageryGCP
> ### Title: ISOImageryGCPCollection
> ### Aliases: ISOImageryGCP
> ### Keywords: ISO collection gcp imagery
> 
> ### ** Examples
> 
>   md <- ISOImageryGCP$new()
>   require(sf)
Loading required package: sf
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘sf’
>   pt <- sf::st_point(c(1,1))
Error in loadNamespace(x) : there is no package called ‘sf’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘Rcpp’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'spam', 'FastGP', 'lamW', 'nabor', 'minqa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'caret', 'rasterVis', 'arm', 'Cubist', 'ranger'

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_textsf
> ### Title: Visualise sf objects with labels
> ### Aliases: geom_textsf geom_labelsf
> 
> ### ** Examples
> 
> ggplot(waterways) +
+  geom_textsf(label = "Forth and Clyde Canal",
+               hjust = 0.62, vjust = -0.3, fill = "#E4E0A3") +
+  lims(x = c(-4.2, -3.9), y = c(55.9, 56))
Error in geom_textsf(label = "Forth and Clyde Canal", hjust = 0.62, vjust = -0.3,  : 
  The package "sf" is required for `geom_textsf()`
Calls: geom_textsf -> <Anonymous>
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘pander’

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: 'geosphere', 'sf'

Packages suggested but not available for checking:
  'devtools', 'mapview', 'tmaptools'

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

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

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

Package suggested but not available for checking: ‘gstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
Package suggested but not available for checking: ‘mapview’
'LazyData' is specified without a 'data' directory
Running examples in ‘geosed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geo_midpoint
> ### Title: Point of Equidistance to Up to Three Longitude, Latitude Points
> ### Aliases: geo_midpoint
> ### Keywords: circle disk enclosing geo latitude longitude sed smallest
> 
> ### ** Examples
> 
> 
> # Load required packages
> require(mapview)
Loading required package: mapview
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mapview’
> require(sp)
Loading required package: sp
> 
> # Create sample geo dataset
> sample_coord <-
+    matrix(
+         c(
+             sample(327131680:419648450, 3) / 10000000,
+             sample(-1147301410:-1241938690, 3) / 10000000
+         ),
+         ncol = 2
+     )
> 
> # Generate circumcenter and radius
> gmp <- geo_midpoint(sample_coord)
> 
> # Find distance to circumcenter
> radius <- geo_point_dist(rbind(sample_coord[1, ], gmp))
> 
> # Create 80 sided polygon based on gmp's center and radius
> gmp_poly <- geo_surround_poly(gmp, radius, 80)
> 
> # Join all the points into a single matrix
> bound_poly <- rbind(sample_coord, as.vector(gmp), gmp_poly)
> 
> # Create SpacialPoints object and pass to mapview for visualization
> mapview(
+     SpatialPoints(
+         bound_poly[,c(2, 1)],
+         proj4string = CRS("+proj=longlat +datum=WGS84")
+     )
+ )
Error in mapview(SpatialPoints(bound_poly[, c(2, 1)], proj4string = CRS("+proj=longlat +datum=WGS84"))) : 
  could not find function "mapview"
Execution halted
Package required but not available: ‘ggrepel’

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

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

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

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

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

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

Package suggested but not available for checking: ‘bayesplot’

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

Packages suggested but not available for checking:
  'RandomFields', 'mapmisc'

Packages which this enhances but not available for checking:
  'INLA', 'diseasemapping'

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

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'sf', 'terra'

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: 'ggspatial', 'raster', 'sf'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cartography', 'DT', 'GWmodel', 'raster', 'shiny', 'shinyalert',
  'shinyBS', 'shinybusy', 'shinydashboard', 'shinyjs', 'shinyWidgets',
  'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rfast2’

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

Package suggested but not available for checking: ‘mice’

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

Package suggested but not available for checking: ‘inti’

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

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

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

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

VignetteBuilder packages required for checking but not installed:
  'knitcitations', 'ggpubr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DT', 'leaflet', 'leafpop', 'plotly', 'shiny', 'shinyalert',
  'shinycssloaders', 'shinyWidgets'
Packages required but not available: 'Rcpp', 'bigmemory', 'RcppEigen'

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', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gestMultiple.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:81-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:84-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestMultiple.Rd:87-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:79-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gestSingle.Rd:81-84: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘shiny’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘GetDFPData2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gstat', 'fda', 'fda.usc'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'plm', 'fixest'
Package required but not available: ‘RLRsim’

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:
  'raster', 'sf', 'terra', 'geosphere', 'plyr', 'animation',
  'rasterVis'

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

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

Package suggested but not available for checking: ‘RGtk2’

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

Package suggested but not available for checking: ‘condSURV’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GFDmcv', 'GFDrmst', 'shinyWidgets', 'shinyMatrix', 'shiny', 'tippy',
  'plyr', 'shinyjs', 'shinythemes'

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

Package suggested but not available for checking: ‘condSURV’

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

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

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

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', 'crul'

Package suggested but not available for checking: ‘vcr’

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

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

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

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

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:
  'ggrepel', 'shiny', 'ggfittext'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

Packages suggested but not available for checking:
  'geosphere', 'ggforce', 'spelling'

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

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘flexsurv’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggamma)
  > 
  > test_check("ggamma")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 22 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_ggamma.R:111:2'): ggamma equals gengamma.orig from flexsurv ────
  Error in `dgengamma.orig(x, b, a, k)`: could not find function "dgengamma.orig"
  Backtrace:
      ▆
   1. └─testthat::expect_equal(...) at test_ggamma.R:111:9
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 22 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘transformr’

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

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

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

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

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

Package suggested but not available for checking: ‘gstat’

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

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.
Packages required but not available: 'dagitty', 'ggraph', 'ggrepel'

Package suggested but not available for checking: ‘spelling’

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

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

Package suggested but not available for checking: ‘fda’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_lm
> ### Title: Regression Diagnostic Plots with ggplot2
> ### Aliases: gg_lm
> 
> ### ** Examples
> 
> model <- lm(mpg ~ wt + am + gear, data = mtcars)
> gg_lm(model)
Error: Package `ggrepel` required for this function to work.
  Please install it by running `install.packages("ggrepel")`.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggforce’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'brms', 'car', 'effects', 'fixest', 'gamm4', 'ggrepel',
  'glmmTMB', 'gt', 'lme4', 'logistf', 'marginaleffects', 'mice',
  'MCMCglmm', 'nestedLogit', 'rstanarm', 'rstantools', 'sdmTMB',
  'survey'
Packages required but not available: 'plyr', 'reshape2', 'plotly'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘zeitgebr’
Packages required but not available:
  'colourpicker', 'miniUI', 'shiny', 'shinyjs'

Package suggested but not available for checking: ‘devtools’

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘spelling’

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

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

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

Packages suggested but not available for checking:
  'concaveman', 'reshape2', 'units'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gf_sf
> ### Title: Mapping with shape files
> ### Aliases: gf_sf
> 
> ### ** Examples
> 
> 
> if (requireNamespace('maps', quietly = TRUE)) {
+   library(maps)
+   world1 <- sf::st_as_sf(map('world', plot = FALSE, fill = TRUE))
+   gf_sf(data = world1)
+ }
Error in loadNamespace(x) : there is no package called ‘sf’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'forecast', 'ggrepel', 'glmnet', 'raster', 'lfda'
Running examples in ‘ggfortify-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.cv.glmnet
> ### Title: Autoplot 'glmnet::cv.glmnet'
> ### Aliases: autoplot.cv.glmnet
> 
> ### ** Examples
> 
> if (requireNamespace("survival", quietly = TRUE)) {
+   autoplot(glmnet::cv.glmnet(data.matrix(Orange[-3]), data.matrix(Orange[3])))
+ }
Error in loadNamespace(x) : there is no package called ‘glmnet’
Calls: autoplot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages suggested but not available for checking: 'ggimage', 'spelling'
Package required but not available: ‘magick’

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: ‘ggfittext’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggtree', 'ggrepel'
Package unavailable to check Rd xrefs: ‘ggtree’
Running examples in ‘gggenomes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pick
> ### Title: Pick bins and seqs by name or position
> ### Aliases: pick pick_seqs pick_seqs_within pick_by_tree
> 
> ### ** Examples
> 
> s0 <- tibble::tibble(
+   bin_id = c("A", "B", "B", "B", "C", "C", "C"),
+   seq_id = c("a1", "b1", "b2", "b3", "c1", "c2", "c3"),
+   length = c(1e4, 6e3, 2e3, 1e3, 3e3, 3e3, 3e3)
+ )
> 
> p <- gggenomes(seqs = s0) + geom_seq(aes(color = bin_id), size = 3) +
+   geom_bin_label() + geom_seq_label() +
+   expand_limits(color = c("A", "B", "C"))
> p
> 
> # remove
> p %>% pick(-B)
> 
> # select and reorder, by ID and position
> p %>% pick(C, 1)
> 
> # use helper function
> p %>% pick(starts_with("B"))
> 
> # pick just some seqs
> p %>% pick_seqs(1, c3)
> 
> # pick with .bin scope
> p %>% pick_seqs(3:1, .bins = C)
> 
> # change seqs in some bins, but keep rest as is
> p %>% pick_seqs_within(3:1, .bins = B)
> 
> # same w/o scope, unaffected bins remain as is
> p %>% pick_seqs_within(b3, b2, b1)
> 
> # Align sequences with and plot next to a phylogenetic tree
> library(patchwork) # arrange multiple plots
> library(ggtree) # plot phylogenetic trees
Error in library(ggtree) : there is no package called ‘ggtree’
Execution halted
Package required but not available: ‘animation’

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

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

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

Package suggested but not available for checking: ‘sf’

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 suggested but not available for checking: ‘spelling’
Package required but not available: ‘magick’

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

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

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

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

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

Packages suggested but not available for checking:
  'gdtools', 'ggrepel', 'sf', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGIRread', 'ActCR', 'read.gt3x'

Package suggested but not available for checking: ‘actilifecounts’

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
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘lme4’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘sf’

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

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

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

Package suggested but not available for checking: ‘plotly’

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

Packages suggested but not available for checking:
  'RSpectra', 'popkin', 'bnpsd'

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

Packages suggested but not available for checking:
  'car', 'NetworkToolbox', 'NetworkComparisonTest'

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

Package suggested but not available for checking: ‘qgraph’

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

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

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

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

Package suggested but not available for checking: ‘ggspatial’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_node_label
> ### Title: Draw (multi-line) labels at nodes
> ### Aliases: geom_node_label geom_node_info geom_node_splitvar
> 
> ### ** Examples
> 
> library(ggparty)
> data("WeatherPlay", package = "partykit")
> sp_o <- partysplit(1L, index = 1:3)
> sp_h <- partysplit(3L, breaks = 75)
> sp_w <- partysplit(4L, index = 1:2)
> pn <- partynode(1L, split = sp_o, kids = list(
+   partynode(2L, split = sp_h, kids = list(
+     partynode(3L, info = "yes"),
+     partynode(4L, info = "no"))),
+   partynode(5L, info = "yes"),
+   partynode(6L, split = sp_w, kids = list(
+     partynode(7L, info = "yes"),
+     partynode(8L, info = "no")))))
> py <- party(pn, WeatherPlay)
> 
> ggparty(py) +
+   geom_edge() +
+   geom_edge_label() +
+   geom_node_label(aes(label = splitvar),
+                   ids = "inner") +
+   geom_node_label(aes(label = info),
+                   ids = "terminal")
> 
> ######################################
> 
> data("TeachingRatings", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Package required but not available: ‘magick’

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

Packages suggested but not available for checking:
  'gganimate', 'magick', 'sf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GGally’
checkRd: (-1) pcp_scale.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pcp_scale.Rd:54-55: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'ALDEx2', 'DESeq2', 'GGally', 'lefser', 'Maaslin2', 'metagenomeSeq',
  'MicrobiomeStat'

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

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

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

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

Quitting from lines 27-37 [unnamed-chunk-1] (ggplotify.Rmd)
Error: processing vignette 'ggplotify.Rmd' failed with diagnostics:
there is no package called 'ggimage'
--- failed re-building ‘ggplotify.Rmd’

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

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

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

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

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

Packages suggested but not available for checking:
  'rxode2', 'nlmixr2', 'lixoftConnectors', 'xgxr'

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:
  'ggtext', 'ggrepel', 'spelling'
Package required but not available: ‘plyr’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QC_Lines
> ### Title: Calculate QC Limits
> ### Aliases: QC_Lines
> 
> ### ** Examples
> 
> #############################################
> #  Example 1: Charts other than "p" or "u"  #
> #############################################
> 
> # Load Libraries ----------------------------------------------------------
>  require(ggQC)
>  require(plyr)
Loading required package: plyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘plyr’
>  require(ggplot2)
Loading required package: ggplot2
> 
> # Setup Data --------------------------------------------------------------
>  set.seed(5555)
>  Process1 <- data.frame(processID = as.factor(rep(1,100)),
+                         metric_value = rnorm(100,0,1),
+                         subgroup_sample=rep(1:20, each=5),
+                         Process_run_id = 1:100)
>  set.seed(5555)
>  Process2 <- data.frame(processID = as.factor(rep(2,100)),
+                         metric_value = rnorm(100,5, 1),
+                         subgroup_sample=rep(1:10, each=10),
+                         Process_run_id = 101:200)
> 
>  Both_Processes <- rbind(Process1, Process2)
> 
> # QC Values For Individuals -----------------------------------------------
>  # All Together
>    QC_Lines(data = Both_Processes$metric_value, method = "XmR")
  xBar_one_LCL    mean xBar_one_UCL mR_LCL        mR   mR_UCL     sigma
1  -0.04192909 2.57306     5.188049      0 0.9830786 3.212701 0.8716631
> 
> 
>  # For Each Process
>    ddply(Both_Processes, .variables = "processID",
+      .fun =function(df){
+        QC_Lines(data = df$metric_value, method = "XmR")
+      }
+    )
Error in ddply(Both_Processes, .variables = "processID", .fun = function(df) { : 
  could not find function "ddply"
Execution halted
Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggQC)
  > #require(plyr)
  > test_check("ggQC")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 124 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_Indv.r:52:1'): (code run outside of `test_that()`) ─────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'plyr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_Indv.r:52:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_xBar_Bar--xBar_rBar_UL_CL--Grouping_FUN.r:111:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'plyr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_xBar_Bar--xBar_rBar_UL_CL--Grouping_FUN.r:111:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 124 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'colourpicker', 'DT', 'GGally', 'ggpmisc', 'ggrepel', 'ggpubr',
  'ggstance', 'plotly', 'shiny', 'shinyjs', 'shinyjqui', 'survminer',
  'shinyFiles'

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

Packages suggested but not available for checking:
  'gganimate', 'sf', 'sfnetworks'

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: 'mixtools', 'ape', 'bgmm'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_cities
> ### Title: Annotate a Map with Roads and Cities
> ### Aliases: stat_cities stat_interstates StatCityRoad StatCities
> ###   StatInterstates
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> data(oregon)
> 
> ggplot(oregon, aes(group=cd_2020)) +
+   geom_district() +
+   stat_interstates(size=1.4, color="#0044aa55") +
+   stat_cities(geom="text", min_pop=130e3, fontface="bold", adjust=0.8) +
+   scale_fill_penn82() +
+   theme_map()
Error in loadNamespace(x) : there is no package called ‘sf’
Calls: geom_district ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘devtools’

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘reshape2’

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

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

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

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

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

Package suggested but not available for checking: ‘hrbrthemes’

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

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tinysnapshot', 'ggrepel'
Running ‘tinytest.R’ [1s/2s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("ggspark")
  + }
  
  test-plot.R...................    0 tests    
  test-plot.R...................    0 tests    
  test-plot.R...................    0 tests    Error: Package tinysnapshot could not be loaded
  Execution halted
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'prettymapr', 'raster', 'terra', 'ggrepel', 'stars', 'lwgeom'

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

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:
  'ggcorrplot', 'ggrepel', 'statsExpressions'

Packages suggested but not available for checking:
  'afex', 'BayesFactor', 'lme4', 'metaBMA', 'metaplus', 'rstantools',
  'WRS2'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_weighted_mean
> ### Title: Compute weighted y mean
> ### Aliases: stat_weighted_mean StatWeightedMean
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("reshape")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
Loading required namespace: reshape
Failed with error:  ‘there is no package called ‘reshape’’
> ## End(Don't show)
> library(ggplot2)
> 
> data(tips, package = "reshape")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘reshape’
Calls: data -> find.package
Execution halted
Package required but not available: ‘survey’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggsurvfit_options
> ### Title: Global Options
> ### Aliases: ggsurvfit_options
> 
> ### ** Examples
> 
> options("ggsurvfit.switch-color-linetype" = TRUE)
> library(tidycmprsk)
Error in library(tidycmprsk) : there is no package called ‘tidycmprsk’
Execution halted
Packages suggested but not available for checking: 'plyr', 'reshape2'
Package required but not available: ‘ggrepel’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pander', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘magick’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
Package suggested but not available for checking: ‘AICcmodavg’
checkRd: (-1) MODFIT.Rd:33: Lost braces; missing escapes or markup?
    33 |   {chisq_i = sum( (O_iz - E_iz)^2 / E_iz; z = 0, ..., C ), }
       |   ^
checkRd: (-1) probs.GGUM.Rd:27: Lost braces; missing escapes or markup?
    27 |   GUM-based probabilities just constrain alpha to a unit vector of length {I}
       |                                                                           ^
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'plotly', 'shiny'
Package required but not available: ‘shiny’

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plyr', 'extraDistr', 'reshape2'

Package suggested but not available for checking: ‘ggraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DESeq2’
Package unavailable to check Rd xrefs: ‘DESeq2’
Package required but not available: ‘Rcpp’

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

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

Package suggested but not available for checking: ‘rnaturalearth’

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

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

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

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

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

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.
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Found the following HTML validation problems:
sample_income_data.html:37:1 (sample_income_data.Rd:8): Warning: trimming empty <h4>
Packages required but not available: 'Rcpp', 'energy', '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: ‘DescTools’

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

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

Packages suggested but not available for checking: 'DAAG', '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.
Packages required but not available: 'geojsonsf', 'sf'

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

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

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

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: ‘crul’

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

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

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

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

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

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

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

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

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: ‘DoubleML’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GeneralisedLambdaDistribution.Rd:60: Lost braces; missing escapes or markup?
    60 |   \code{gpd} uses GPD parameterisation, see {van Staden and Loots (2009)}
       |                                             ^
checkRd: (-1) gld.lmoments.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.lmoments.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.lmoments.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.lmoments.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gld.moments.Rd:14: Lost braces
    14 |   {\eqn{\lambda_1}{lambda 1} location parameter}
       |   ^
checkRd: (-1) gld.moments.Rd:15: Lost braces
    15 |   {\eqn{\lambda_2}{lambda 2} - scale parameter}
       |   ^
checkRd: (-1) gld.moments.Rd:16: Lost braces
    16 |   {\eqn{\lambda_3}{lambda 3} - first shape parameter}
       |   ^
checkRd: (-1) gld.moments.Rd:17: Lost braces
    17 |   {\eqn{\lambda_4}{lambda 4} - second shape parameter}
       |   ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘GLDEX’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NEWS.Rd:16: Lost braces; missing escapes or markup?
    16 |         \item Now \code{AICc == Inf} when {n <= p + 1}.
       |                                           ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
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checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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checkRd: (-1) summarylr.Rd:34: Lost braces
    34 | \item{method}{NULL or character vector of length 0, 1 or 2; may be code{"LRT"} or \code{"Rao"} or \code{c("LRT", "Rao")} to compute specified P-values.
       |                                                                        ^
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [19s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(glmglrt)
  > 
  > test_check("glmglrt")
  [ FAIL 1 | WARN 54 | SKIP 0 | PASS 241 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-confint_contrast.R:141:2'): confint_contrast with Wald's formula on many other models ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lmerTest'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-confint_contrast.R:141:9
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 54 | SKIP 0 | PASS 241 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'effects', 'DHARMa'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggforce', 'glmmTMB', 'lme4'

Packages suggested but not available for checking:
  'cosinor', 'DHARMa', 'DT', 'flextable', 'ftExtra'

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

Package suggested but not available for checking: ‘mlmRev’

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

Package suggested but not available for checking: ‘bayesplot’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Packages required but not available:
  'lme4', 'bigmemory', 'Rcpp', 'reshape2', 'rstan', 'rstantools',
  'RcppArmadillo', 'RcppEigen', 'StanHeaders'

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

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

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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'car', 'ggpubr', 'glmmTMB', 'lme4', 'lmerTest', 'plotly', 'qvalue'

Package suggested but not available for checking: ‘DESeq2’

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

Packages suggested but not available for checking:
  'mlmRev', 'reshape2', 'car', 'DHARMa', 'effects', 'dotwhisker',
  'plyr', 'blme', 'ade4', 'ape'

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', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'smoof', 'mlrMBO', 'torch', 'aorsf'

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: ‘glmnet’

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

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                            ^
checkRd: (-1) ccancer.Rd:16: Lost braces
    16 |                          a factor with levels either \\code{F} (female) or code{M} (male)}
       |                                                                                ^
checkRd: (-1) galapagos.Rd:4: Lost braces
     4 | \title{{Gal\'{a}pagos} Island species data}
       |              ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                ^
checkRd: (-1) galapagos.Rd:6: Lost braces
     6 |   The number of species on the {Gal\'{a}pagos} Islands
       |                                      ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |    ^
checkRd: (-1) galapagos.Rd:40: Lost braces
    40 |    {Gal\'{a}pagos} (the endemics). 
       |          ^
checkRd: (-1) galapagos.Rd:44: Lost braces
    44 |   Species number and endemism: The {Gal\'{a}pagos} Archipelago revisited.
       |                                          ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cplm’

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

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

Package suggested but not available for checking: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
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checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:14: Lost braces
    14 |   \item{object}{A fitted model object, of class \code{glm}, \code{lm} or code{glm.nb}}
       |                                                                              ^
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-methods.Rd:14: Lost braces
    14 | code{glmulti} finds what are the \code{n} best models (the confidence set of models) among all possible models (the candidate set, as specified by the user).
       |     ^
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'forecast', 'gtrendsR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fxregime’
Unavailable namespace imported from by a ':::' call: ‘fxregime’
  See the note in ?`:::` about the use of this operator.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'bs4Dash', 'shiny', 'DT', 'GeoThinneR', 'leaflet', 'mcp', 'pROC',
  'sf', 'shinyWidgets', 'terra', 'tidyterra', 'waiter'

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

Packages suggested but not available for checking:
  'mapedit', 'plotly', 's2'

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: 'magick', 'qs2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getRiiGLPK.Rd:35: Lost braces; missing escapes or markup?
    35 |   Returns the current scale factor $r_{ii}$ for row \code{i} of the specified
       |                                       ^
checkRd: (-1) getSjjGLPK.Rd:35: Lost braces; missing escapes or markup?
    35 |   Returns the current scale factor $s_{jj}$ for column \code{j} of the
       |                                       ^
checkRd: (-1) setRiiGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $r_{ii}$.
       |                     ^
checkRd: (-1) setSjjGLPK.Rd:28: Lost braces; missing escapes or markup?
    28 |     Scale factor $s_{jj}$.
       |                     ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'ape', 'mvSLOUCH'
Running examples in ‘GLSME-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GLSME-package
> ### Title: Generalized Least Squares with Measurement Error
> ### Aliases: GLSME-package
> ### Keywords: generalized least squares regression measurement error
> 
> ### ** Examples
> 
> n<-3 ## number of species
> apetree<-ape::rtree(n)
Error in loadNamespace(x) : there is no package called ‘ape’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

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:
  'shiny', 'shinydashboard', 'shinyBS', 'DT'

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

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', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'JMbayes2', 'registr', 'funData', 'MFPCA', 'MJMbamlss', 'refund'
Running examples in ‘gmfamm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mface_cyc
> ### Title: Multilevel functional principal components analysis with fast
> ###   covariance estimation
> ### Aliases: mface_cyc
> 
> ### ** Examples
> 
> require(refund)
Loading required package: refund
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘refund’
> data(DTI)
Warning in data(DTI) : data set ‘DTI’ not found
> mfpca.DTI <- mfpca.face(Y = DTI$cca, id = DTI$ID, twoway = TRUE)
Error in mfpca.face(Y = DTI$cca, id = DTI$ID, twoway = TRUE) : 
  could not find function "mfpca.face"
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gstat', 'compositions'

Package suggested but not available for checking: ‘DescTools’

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', '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: ‘SeqVarTools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
checkRd: (-1) ATEgel.Rd:24: Lost braces
    24 | \item{g}{A formula as \code{y~z}, where code{y} is the response and
       |                                             ^
Note: skipping ‘gmm_with_R.rnw’ due to unavailable dependencies: 'car'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'AER', 'car'
Running examples in ‘gmnl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AIC.gmnl
> ### Title: Akaike's Information Criterion
> ### Aliases: AIC.gmnl BIC.gmnl
> 
> ### ** Examples
> 
> 
> ## Estimate MNL model
> data("TravelMode", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘lme4’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggrepel', 'geometry', 'Rfast', 'plyr'

Packages suggested but not available for checking: 'pdftools', 'webshot2'

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

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘simts’

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: 'ggforce', 'ggpubr', 'wordcloud'

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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'keras', 'tensorflow'

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

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

Package suggested but not available for checking: ‘fgsea’

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

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

Packages suggested but not available for checking:
  'vegdata', 'BiodiversityR'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
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checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'devtools', 'pixiedust', 'ggraph', 'migraph', 'manynet'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘GoodmanKruskal.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/GoodmanKruskal.Rcheck/vign_test/GoodmanKruskal/vignettes/GoodmanKruskal_files/figure-html/unnamed-chunk-4-1.png
720x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 84579 bytes
Input file size = 84777 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 70645
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 70645

Output IDAT size = 70645 bytes (13934 bytes decrease)
Output file size = 70723 bytes (14054 bytes = 16.58% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/GoodmanKruskal.Rcheck/vign_test/GoodmanKruskal/vignettes/GoodmanKruskal_files/figure-html/unnamed-chunk-5-1.png
720x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 96149 bytes
Input file size = 96359 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 79566
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 79566

Output IDAT size = 79566 bytes (16583 bytes decrease)
Output file size = 79644 bytes (16715 bytes = 17.35% decrease)


Quitting from lines 148-151 (GoodmanKruskal.Rmd)
Error: processing vignette 'GoodmanKruskal.Rmd' failed with diagnostics:
object 'Greene' not found
--- failed re-building ‘GoodmanKruskal.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cld2', 'tidytext', 'tm', 'topicmodels'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cld2', 'shiny', 'shinyjs'
checkRd: (-1) gl_nlp.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gl_nlp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'promises'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'googleway', 'sf', 'webshot2', 'raster', 'schemr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) compute_lower_bound_1tree.Rd:31: Lost braces; missing escapes or markup?
    31 | instance from vertex 1.  Internally, it creates the graph Kn-{v1}
       |                                                              ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'BradleyTerry2', 'DescTools', 'ggrepel', 'PlackettLuce'

Packages suggested but not available for checking:
  'climatrends', 'ClimMobTools', 'chirps'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reticulate’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggraph’

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

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

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

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

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

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

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gpkg_table_pragma
> ### Title: Lazy Access to Tables by Name
> ### Aliases: gpkg_table_pragma gpkg_table_pragma.character
> ###   gpkg_table_pragma.SQLiteConnection gpkg_table_pragma.geopackage
> ###   gpkg_table gpkg_table.default gpkg_collect gpkg_tbl gpkg_rast
> ###   gpkg_vect
> 
> ### ** Examples
> 
> ## Don't show: 
> if (!inherits(try(requireNamespace("RSQLite", quietly = TRUE)), 'try-error') &&!inherits(try(requireNamespace("dbplyr", quietly = TRUE)), 'try-error') && !inherits(try(requireNamespace("terra", quietly = TRUE)), 'try-error')) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
> ## End(Don't show)
> 
> tf <- tempfile(fileext = ".gpkg")
> 
> r <- terra::rast(system.file("extdata", "dem.tif", package = "gpkg"))
Error in loadNamespace(x) : there is no package called ‘terra’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘tinytest.R’ [1s/2s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("gpkg")
  + }
  
  test_gpkg.R...................    0 tests    
  test_gpkg.R...................    0 tests    Error in eval(expr, envir = e) : 
    requireNamespace("terra", quietly = TRUE) is not TRUE
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> stopifnot
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown

Quitting from lines 35-61 [unnamed-chunk-2] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘intro.Rmd’

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

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

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

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

Package suggested but not available for checking: ‘RcppArmadillo’

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

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: ‘rstan’

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'shiny', 'shiny.i18n', 'waiter'

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

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

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

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

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

Package suggested but not available for checking: ‘plumber’

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

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

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

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.
Malformed Title field: should not end in a period.
checkRd: (-1) grade-package.Rd:51-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:58-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grade-package.Rd:79-81: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘shiny’

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

Package suggested but not available for checking: ‘pbkrtest’

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

Package suggested but not available for checking: ‘quanteda.textmodels’

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

Package suggested but not available for checking: ‘gRim’

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

Package suggested but not available for checking: ‘spelling’

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

Packages suggested but not available for checking:
  'Seurat', 'ggrepel', 'DESeq2', 'clusterProfiler', 'fgsea',
  'rclipboard', 'cubature', 'DT', 'shinyjs', 'shinyjqui', 'monocle',
  'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Granger.inference.difference.Rd:65: Lost braces; missing escapes or markup?
    65 |         least one root larger than one) on bootstrapped \verb{x} and {y}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:68: Lost braces; missing escapes or markup?
    68 |         least one root larger than one) on bootstrapped \verb{x} and {z}.
       |                                                                      ^
checkRd: (-1) Granger.inference.difference.Rd:71: Lost braces; missing escapes or markup?
    71 |         least one root larger than one) on bootstrapped \verb{x}, \verb{y} and {z}.
       |                                                                                ^
Package required but not available: ‘car’

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

Package suggested but not available for checking: ‘shinytest’

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

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

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

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: ‘googlePolylines’

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

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: 'osqp', 'glmnet', 'edmcr', 'CVXR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'gMCP', 'gt', 'lrstat'
Running ‘testthat.R’ [72s/86s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(graphicalMCP)
  > 
  > test_check("graphicalMCP")
  [ FAIL 1 | WARN 0 | SKIP 14 | PASS 147 ]
  
  ══ Skipped tests (14) ══════════════════════════════════════════════════════════
  • On CRAN (12): 'test-print.graph_report.R:4:3',
    'test-print.graph_report.R:14:3', 'test-print.graph_report.R:49:3',
    'test-print.graph_report.R:62:3', 'test-print.graph_report.R:68:3',
    'test-print.initial_graph.R:2:3', 'test-print.initial_graph.R:12:3',
    'test-print.power_report.R:5:3', 'test-print.power_report.R:15:3',
    'test-print.power_report.R:30:3', 'test-print.power_report.R:58:3',
    'test-print.updated_graph.R:12:3'
  • empty test (2): 'test-graph_test_closure.R:228:1',
    'test-graph_test_closure.R:257:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-graph_generate_weights.R:11:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'gMCP'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-graph_generate_weights.R:11:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 14 | PASS 147 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'glmnet', 'qgraph', 'RcppArmadillo'

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

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

Package suggested but not available for checking: ‘uwot’

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

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

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

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

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

Packages suggested but not available for checking:
  'gamm4', 'lme4', 'GJRM', 'glmmTMB', 'ggdist', 'sf'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'feasts', 'forecast', 'GA', 'shiny', 'tsfeatures', 'tsibble'

Package suggested but not available for checking: ‘shinydashboard’

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

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

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

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

Package suggested but not available for checking: ‘tsibbledata’

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

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

Package suggested but not available for checking: ‘fields’

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

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: 'gRbase', 'Rcpp', 'RcppArmadillo'

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

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

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

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

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', 'survey'

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

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 required but not available: 'FME', 'reshape2', 'sf', 'tmap'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) covFun.Rd:89-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:91-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:93-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:96-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:98-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:100-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) covFun.Rd:116-117: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'blockmodels', 'aricode'

Package suggested but not available for checking: ‘spelling’

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

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

Package suggested but not available for checking: ‘spelling’

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

Package suggested but not available for checking: ‘spelling’

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

Packages suggested but not available for checking:
  'bayesplot', 'cramer', 'DiagrammeRsvg', 'extraDistr', 'fields',
  'spelling'

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

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

Package suggested but not available for checking: ‘smooth’

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

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'

Package suggested but not available for checking: ‘rdd’

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: 'fields', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'magick', 'pdftools'
Packages required but not available: 'Rcpp', 'Ckmeans.1d.dp', 'dqrng'

Package suggested but not available for checking: ‘FunChisq’

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: ‘sf’

Package suggested but not available for checking: ‘magick’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NEWS.Rd:669: Lost braces; missing escapes or markup?
   669 |     parameters are rounded so they belong to one of {0, 0.5, 1}. (Simon)
       |                                                     ^
checkRd: (-1) gradients.Rd:96-99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:100-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gradients.Rd:104-107: Lost braces in \itemize; meant \describe ?
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:
  'gRain', 'gRbase', 'Rcpp', 'RcppArmadillo', 'RcppEigen'

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

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

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

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

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

Package suggested but not available for checking: ‘phangorn’

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

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: ‘car’

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

Packages suggested but not available for checking: 'lmerTest', 'xpectr'

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

Package suggested but not available for checking: ‘snplist’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘binGroup2’

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', 'spam', 'reshape2', 'RcppArmadillo'

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

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) matches.Rd:33: Lost braces; missing escapes or markup?
    33 | be set to an index value of \code{length+1}.  If {indexes=FALSE}, they will
       |                                                  ^
Packages required but not available:
  'shiny', 'shinyWidgets', 'DT', 'mirt', 'sirt', 'flextable', 'gt',
  'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GRS.Powerfunc.Rd:22: Lost braces
    22 | {Power: }{Matrix of power values plotted}
       |          ^
Packages required but not available: 'glmnet', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
checkRd: (-1) qdb.p.correct.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{refpts}{a numeric vector used as a reference point to determine the correct side of the \code{qdb} for classifying \code{x}. The \code{length(refpts)} should be equal to {ncol(x)}. Default to \code{colMeans(x)}. }
       |                                                                                                                                                                                 ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'trend'

Package suggested but not available for checking: ‘sf’

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

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

Package suggested but not available for checking: ‘missSBM’

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

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

Package suggested but not available for checking: ‘gsDesign’

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

Package suggested but not available for checking: ‘simtrial’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ade4’
Running examples in ‘gSeg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gSeg
> ### Title: Graph-Based Change-Point Detection
> ### Aliases: gSeg
> 
> ### ** Examples
> 
> 
> data(Example)
> # Five examples, each example is a n-length sequence.
> # Ei (i=1,...,5): an edge matrix representing a similarity graph constructed on the
> # observations in the ith sequence.  
> # The following code shows how the Ei's were constructed.
> 
> require(ade4) 
Loading required package: ade4
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ade4’
> # For illustration, we use 'mstree' in this package to construct the similarity graph.
> # You can use other ways to construct the graph.
> 
> ## Sequence 1: change in mean in the middle of the sequence.
> d = 50
> mu = 2
> tau = 100
> n = 200
> set.seed(500)
> y = rbind(matrix(rnorm(d*tau),tau), matrix(rnorm(d*(n-tau),mu/sqrt(d)), n-tau))
> y.dist = dist(y)
> E1 = mstree(y.dist)
Error in mstree(y.dist) : could not find function "mstree"
Execution halted
Packages required but not available: 'SAM', 'penalized'

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

Package suggested but not available for checking: ‘qpdf’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following HTML validation problems:
gsheet2tbl.html:31:5 (gsheet2tbl.Rd:20): Warning: trimming empty <p>
gsheet2tbl.html:31:1 (gsheet2tbl.Rd:20): Warning: trimming empty <li>
Package required but not available: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) lisiecki2005.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lisiecki2005.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:25: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) spratt2016.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spratt2016.Rd:29: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'FactoMineR', 'reshape2'

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

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: 'sf', 'sftime', 'stars'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) artset1987.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tumor.Rd:12: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) gte.Rd:98: Lost braces; missing escapes or markup?
    98 | \code{left} and {right} for illustrative purpose), one would need a third variable (\code{status}) taking the value 0 
       |                 ^
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ade4’
Running examples in ‘gTestsMulti-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gTestsMulti
> ### Title: New graph-based multi-sample tests
> ### Aliases: gTestsMulti-package
> 
> ### ** Examples
> 
> 
> ## Mean difference in Gaussian distribution.
> d = 50
> mu = 0.2
> sam = 50
> 
> set.seed(500)
> X1 = matrix(rnorm(d*sam), sam)
> X2 = matrix(rnorm(d*sam,mu), sam)
> X3 = matrix(rnorm(d*sam,2*mu), sam)
> 
> data_list = list(X1, X2, X3)
> 
> # We use 'mstree' in 'ade4' package to construct the minimum spanning tree.
> require(ade4)
Loading required package: ade4
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ade4’
> x = rbind(X1, X2, X3)
> E = mstree(dist(x))
Error in mstree(dist(x)) : could not find function "mstree"
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ade4’

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

Package suggested but not available for checking: ‘webshot2’

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

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

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

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

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

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

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

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

Packages suggested but not available for checking:
  'katex', 'magick', 'shiny', 'webshot2'

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

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

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

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

Packages suggested but not available for checking:
  'car', 'flextable', 'lme4', 'mice', 'openxlsx', 'spelling', 'survey'

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

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'sf', 'spdep', 'ade4', 'adegraphics', 'adespatial', 'car', 'effects',
  'ggrepel', 'heplots', 'candisc'
Running examples in ‘Guerry-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Guerry
> ### Title: Data from A.-M. Guerry, "Essay on the Moral Statistics of
> ###   France"
> ### Aliases: Guerry
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MultiSpat.Rmd’ using rmarkdown

Quitting from lines 41-47 [unnamed-chunk-1] (MultiSpat.Rmd)
Error: processing vignette 'MultiSpat.Rmd' failed with diagnostics:
there is no package called 'ade4'
--- failed re-building ‘MultiSpat.Rmd’

--- re-building ‘guerry-multivariate.Rmd’ using rmarkdown

Quitting from lines 52-63 [load] (guerry-multivariate.Rmd)
Error: processing vignette 'guerry-multivariate.Rmd' failed with diagnostics:
there is no package called 'car'
--- failed re-building ‘guerry-multivariate.Rmd’

SUMMARY: processing the following files failed:
  ‘MultiSpat.Rmd’ ‘guerry-multivariate.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
checkRd: (-1) PLSSVD.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
checkRd: (-1) guidedPLS.Rd:33: Lost braces; missing escapes or markup?
    33 | The number of low-dimension (k < {N, M, L, O}, Default: .minDim(X1, X2, Y1, Y2))
       |                                  ^
checkRd: (-1) sPLSDA.Rd:24: Lost braces; missing escapes or markup?
    24 | The number of low-dimension (k < {N, M, L}, Default: .minDim(X, Y))
       |                                  ^
Error(s) in re-building vignettes:
  ...
--- re-building ‘guidedPLS-1.Rmd’ using rmarkdown

Quitting from lines 33-38 [data2] (guidedPLS-1.Rmd)
Error: processing vignette 'guidedPLS-1.Rmd' failed with diagnostics:
there is no package called 'fields'
--- failed re-building ‘guidedPLS-1.Rmd’

--- re-building ‘guidedPLS-2.Rmd’ using rmarkdown

Quitting from lines 33-38 [data2] (guidedPLS-2.Rmd)
Error: processing vignette 'guidedPLS-2.Rmd' failed with diagnostics:
there is no package called 'fields'
--- failed re-building ‘guidedPLS-2.Rmd’

SUMMARY: processing the following files failed:
  ‘guidedPLS-1.Rmd’ ‘guidedPLS-2.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘quarto’
checkRd: (-1) guild_merge.Rd:38: Lost braces; missing escapes or markup?
    38 |     \item{\code{summary_name}}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                                     ^
checkRd: (-1) guild_merge_cli.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{summary_name}{Name used for the run summary. Use '${run_id}' in the name to include the run ID.}
       |                                                          ^
Package required but not available: ‘Rcpp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘RRprof.out’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

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

Packages suggested but not available for checking: 'ade4', 'ggpubr'

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

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

Package suggested but not available for checking: ‘tidytext’

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

Packages suggested but not available for checking: 'adaptMCMC', 'drc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'eda4treeR', 'lme4'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) esSim.Rd:81: Lost braces; missing escapes or markup?
    81 | \eqn{83} SNPs are in cluster {-}, \eqn{714} SNPs are in cluster \eqn{0},
       |                              ^
checkRd: (-1) esSimDiffPriors.Rd:91: Lost braces; missing escapes or markup?
    91 | \eqn{64} SNPs are in cluster {-}, \eqn{708} SNPs are in cluster \eqn{0},
       |                              ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggrepel’

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

Package suggested but not available for checking: ‘glmnet’

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

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

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leaflet', 'leaflet.extras', 'nhdplusTools', 'sf', 'shiny',
  'promises', 'miniUI', 'shinyWidgets', 'units', 'elevatr', 'terra'

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', 'lmomco', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following HTML validation problems:
gedit.html:139:6 (gedit.Rd:72): Warning: trimming empty <p>
gedit.html:139:1 (gedit.Rd:72): Warning: trimming empty <li>
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:285: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:286-293: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gWidgets2tcltk-undocumented.Rd:378: Lost braces
   378 | \item{visible}{logical. If code{TRUE} window is drawn when
       |                                ^
Packages required but not available: 'plotly', 'RcppRoll', 'shiny'

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

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

Package suggested but not available for checking: ‘gstat’

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:
  'golem', 'shiny', 'DT', 'shinydashboard', 'sf', 'plotly', 'leaflet',
  'shinyjs', 'Rcpp'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Packages required but not available: 'Rcpp', 'prodlim', 'RcppArmadillo'

Package suggested but not available for checking: ‘BinaryDosage’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DT', 'plotly'
Packages required but not available: 'geojsonsf', 'sf', 'V8'

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

Package suggested but not available for checking: ‘spelling’

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

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

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

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

Packages suggested but not available for checking:
  'spelling', 'pander', 'shinycssloaders', 'shinyhelper', 'shinyjs'

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

Package suggested but not available for checking: ‘ape’

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

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: ‘hal9001’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'lmerTest'
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
Packages required but not available: 'shiny', 'shinyWidgets'

Package suggested but not available for checking: ‘shinytest2’

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

Package suggested but not available for checking: ‘jsonld’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'magick', 'mc2d', 'Rcpp', 'reshape2', 'Rfast', '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: 'car', 'olsrr', 'ggpubr', 'devtools'

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: ‘caret’

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

Package suggested but not available for checking: ‘openxlsx’

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

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

Package suggested but not available for checking: ‘tmap’

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:
  'daltoolbox', 'tsmp', 'dtwclust', 'rugarch', 'forecast', 'hht'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: default_recipe_blueprint
> ### Title: Default recipe blueprint
> ### Aliases: default_recipe_blueprint mold.recipe
> 
> ### ** Examples
> 
> library(recipes)
Error in library(recipes) : there is no package called ‘recipes’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘forge.Rmd’ using rmarkdown

Quitting from lines 165-173 [unnamed-chunk-10] (forge.Rmd)
Error: processing vignette 'forge.Rmd' failed with diagnostics:
there is no package called 'recipes'
--- failed re-building ‘forge.Rmd’

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

Quitting from lines 215-226 [unnamed-chunk-19] (mold.Rmd)
Error: processing vignette 'mold.Rmd' failed with diagnostics:
there is no package called 'recipes'
--- failed re-building ‘mold.Rmd’

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

Quitting from lines 280-292 [unnamed-chunk-13] (package.Rmd)
Error: processing vignette 'package.Rmd' failed with diagnostics:
there is no package called 'recipes'
--- failed re-building ‘package.Rmd’

SUMMARY: processing the following files failed:
  ‘forge.Rmd’ ‘mold.Rmd’ ‘package.Rmd’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ape’
Error(s) in re-building vignettes:
  ...
--- re-building ‘harmonicmeanp.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/harmonicmeanp.Rcheck/vign_test/harmonicmeanp/vignettes/harmonicmeanp_files/figure-html/winplot-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 71411 bytes
Input file size = 71585 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 58082
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 58082

Output IDAT size = 58082 bytes (13329 bytes decrease)
Output file size = 58160 bytes (13425 bytes = 18.75% decrease)


Quitting from lines 389-401 [fiddler] (harmonicmeanp.Rmd)
Error: processing vignette 'harmonicmeanp.Rmd' failed with diagnostics:
there is no package called 'ape'
--- failed re-building ‘harmonicmeanp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

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
GNU make is a SystemRequirements.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) deff.sigma.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deff.sigma.Rd:35: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'mcmcsae', 'survey'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘RcppArmadillo’

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

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

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

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: ‘rARPACK’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdf5r.Rmd’ using rmarkdown

Quitting from lines 86-92 [unnamed-chunk-4] (hdf5r.Rmd)
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘hdf5r.Rmd’

SUMMARY: processing the following file failed:
  ‘hdf5r.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Rcpp', 'reshape2', '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: 'missRanger', 'plyr'

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: 'NPCirc', 'Directional'

Package suggested but not available for checking: ‘DirStats’

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', 'RcppEnsmallen'

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', 'dqrng', 'RcppEigen'

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

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

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

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: ‘qvalue’

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

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: 'devtools', 'spelling'

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

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘spelling’

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

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

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

Packages suggested but not available for checking:
  'timetk', 'plotly', 'uwot'

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

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

Packages suggested but not available for checking:
  'healthyR.ai', 'forecast', 'tidymodels', 'tune', 'glmnet', 'smooth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'healthyR', 'healthyR.ts', 'healthyR.ai', 'TidyDensity', 'tidyAML',
  'RandomWalker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Malformed Title field: should not end in a period.
checkRd: (-1) colByValue.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.}
       |                       ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plotly', 'reshape2'

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

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

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

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

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

Packages suggested but not available for checking: 'BCEA', 'flexsurv'

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

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

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

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

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:
  'lme4', 'fields', 'shiny', 'shinyWidgets'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

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

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

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

Packages suggested but not available for checking:
  'candisc', 'effects', 'reshape', 'reshape2', 'animation',
  'mvinfluence'

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

Packages suggested but not available for checking:
  'leafpop', 'lwgeom', 'mapview'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) marker_h2.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:96-97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) marker_h2_means.Rd:102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:41-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) repeatability.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'cplm', 'DESeq2', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) glm.hermite.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glm.hermite.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
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    38 |   {b} and \code{m} to be lower (or greater) than \code{q}.
       |   ^
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manual.
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manual.
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manual.
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--- re-building ‘clarke_wright_performance.Rmd’ using rmarkdown

Quitting from lines 20-38 [setup] (clarke_wright_performance.Rmd)
Error: processing vignette 'clarke_wright_performance.Rmd' failed with diagnostics:
there is no package called 'ggExtra'
--- failed re-building ‘clarke_wright_performance.Rmd’

SUMMARY: processing the following file failed:
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    20 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
checkRd: (-1) predictPairInternal.Rd:18: Lost braces; missing escapes or markup?
    18 | A number in the set {-1, 0, 1}, where 1 means row1 is predicted to
       |                     ^
Error(s) in re-building vignettes:
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--- re-building ‘README.Rmd’ using rmarkdown
--- finished re-building ‘README.Rmd’

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Quitting from lines 99-108 [unnamed-chunk-7] (cross-validation.Rmd)
Error: processing vignette 'cross-validation.Rmd' failed with diagnostics:
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--- re-building ‘how-to-make-heuristic.Rmd’ using rmarkdown

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SUMMARY: processing the following files failed:
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  ‘reproducing-results.Rmd’

Error: Vignette re-building failed.
Execution halted
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
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Found the following HTML validation problems:
get_breaks.html:78:1 (get_breaks.Rd:37): Warning: trimming empty <dt>
Packages required but not available: 'sf', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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manual.
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manual.
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manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) hierNet.Rd:28: Lost braces; missing escapes or markup?
    28 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |               ^
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    30 |     terms, th_{jj}X_j^2, in the model.  Default TRUE.}  
       |               ^
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    63 | \seealso{\link{predict.hierNet.logistic},link{hierNet.logistic.path}}
       |                                              ^
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    39 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
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    38 |   terms, th_{jj}X_j^2, in the model.  Default TRUE.}
       |             ^
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Specified C++11: please drop specification unless essential
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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manual.
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manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'ape', 'phytools', 'diversitree', 'paleotree', 'geiger', 'phangorn',
  'TreeSim', 'corHMM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'reshape', 'plyr', 'car', 'heplots', 'effects'
Running examples in ‘HistData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CushnyPeebles
> ### Title: Cushny-Peebles Data: Soporific Effects of Scopolamine
> ###   Derivatives
> ### Aliases: CushnyPeebles CushnyPeeblesN
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(CushnyPeebles)
> # quick looks at the data
> plot(CushnyPeebles)
> boxplot(CushnyPeebles, ylab="Hours of Sleep", xlab="Treatment")
> 
> ##########################
> # Repeated measures MANOVA
> 
> CPmod <- lm(cbind(Control, L_hyoscyamine, L_hyoscine, DL_hyoscine) ~ 1, data=CushnyPeebles)
> 
> # Assign within-S factor and contrasts
> Treatment <- factor(colnames(CushnyPeebles), levels=colnames(CushnyPeebles))
> contrasts(Treatment) <- matrix(
+ 	c(-3, 1, 1, 1,
+ 	   0,-2, 1, 1,
+ 	   0, 0,-1, 1), ncol=3)
> colnames(contrasts(Treatment)) <- c("Control.Drug", "L.DL", "L_hy.DL_hy")
> 
> Treats <- data.frame(Treatment)
> if (require(car)) {
+ (CPaov <- Anova(CPmod, idata=Treats, idesign= ~Treatment))
+ }
Loading required package: car
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘car’
> summary(CPaov, univariate=FALSE)
Error: object 'CPaov' not found
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'FactoMineR', 'Rcpp', 'RcppArmadillo'

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

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

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

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

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

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', 'bayesplot', 'rstantools', 'RcppArmadillo'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'mice', 'plotly', 'plyr', 'latticeExtra', 'gt', 'qs'
html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'mc2d', 'cubature'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) nafracCalc.Rd:45: Lost braces
    45 |   as if code{y} were not of class \code{"multipleHmmDataSets"}.
       |             ^
Skipping checking math rendering: package 'V8' unavailable
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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manual.
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manual.
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manual.
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Running examples in ‘hnp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cbb
> ### Title: Coffee berry borer trapping data
> ### Aliases: cbb
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(cbb)
> # exploratory plot
> require(latticeExtra)
Loading required package: latticeExtra
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘latticeExtra’
> trellis.par.set(strip.background=list(col="lightgrey"))
Error in trellis.par.set(strip.background = list(col = "lightgrey")) : 
  could not find function "trellis.par.set"
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'bamsignals', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) HOasso.Rd:43: Lost braces; missing escapes or markup?
    43 | Arguments \code{x} and {y} are \code{character} objects and can assume values   \code{"sout"}, \code{"dout"}, \code{"lout"}, \code{"sin"}, \code{"din"}, \code{"lin"} representing the out-strength, out-degree, out-log-strength, in-strength, in-degree, and in-log-strength respectively.
       |                        ^
Package required but not available: ‘treemapify’

Package suggested but not available for checking: ‘spelling’

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

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

Quitting from lines 25-29 [unnamed-chunk-1] (simulating-data.Rmd)
Error: processing vignette 'simulating-data.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building ‘simulating-data.Rmd’

SUMMARY: processing the following file failed:
  ‘simulating-data.Rmd’

Error: Vignette re-building failed.
Execution halted
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  'shinybusy', 'shinyjs', 'shinyvalidate', 'shinyWidgets', 'tippy',
  'mixOmics', 'ggrepel', 'RSpectra', 'reshape2'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: logiths
> ### Title: Horseshoe shrinkage prior in Bayesian Logistic regression
> ### Aliases: logiths
> 
> ### ** Examples
> 
> 
> burnin <- 100
> nmc    <- 500
> thin <- 1
> 
>  
> p <- 100  # number of predictors
> ntrain <- 250  # training size
> ntest  <- 100   # test size
> n <- ntest + ntrain  # sample size
> q <- 10   # number of true predictos
> 
> beta.t <- c(sample(x = c(1, -1), size = q, replace = TRUE), rep(0, p - q))  
> x <- mvtnorm::rmvnorm(n, mean = rep(0, p), sigma = diag(p))    
> 
> zmean <- x %*% beta.t
> z <- rbinom(n, size = 1, prob = boot::inv.logit(zmean))
> X <- scale(as.matrix(x))  # standarization
> 
> 
> # Training set
> ztrain <- z[1:ntrain]
> Xtrain  <- X[1:ntrain, ]
> 
> # Test set
> ztest <- z[(ntrain + 1):n]
> Xtest  <- X[(ntrain + 1):n, ]
> 
> posterior.fit <- logiths(z = ztrain, X = Xtrain, method.tau = "halfCauchy",
+                          burn = burnin, nmc = nmc, thin = 1,
+                          Xtest = Xtest)
Markov chain monte carlo is running
Error in loadNamespace(x) : there is no package called ‘pgdraw’
Calls: logiths ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'units'

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

Packages suggested but not available for checking:
  'shiny', 'shinyWidgets', 'shinydashboard', 'DT', 'shinyalert',
  'shinyjs', 'pander', 'golem'

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

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

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

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

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

Packages suggested but not available for checking: 'jomo', 'Amelia'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fields', 'ranger'
checkRd: (-1) HPLB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HPLB.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Running examples in ‘HPLB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HPLB
> ### Title: High Probability Lower Bounds (HPLB) for the Total Variation
> ###   Distance (TV) Based on Finite Samples
> ### Aliases: HPLB
> 
> ### ** Examples
> 
> ## libs
> library(HPLB)
> library(ranger)
Error in library(ranger) : there is no package called ‘ranger’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘gdtools’

Package suggested but not available for checking: ‘hunspell’

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

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

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 suggested but not available for checking: ‘fields’
Packages suggested but not available for checking:
  'ape', 'lme4', 'wordcloud'
Packages suggested but not available for checking:
  'ape', 'lme4', 'mice', 'sf', 'wordcloud'
Note: skipping ‘Ch_analysing_longitudinal_dataI.Rnw’ due to unavailable dependencies:
  'lme4'
Note: skipping ‘Ch_analysing_longitudinal_dataII.Rnw’ due to unavailable dependencies:
  'lme4'
Note: skipping ‘Ch_analysis_of_variance.Rnw’ due to unavailable dependencies:
  'wordcloud'
Note: skipping ‘Ch_gam.Rnw’ due to unavailable dependencies: 'wordcloud'
Note: skipping ‘Ch_graphical_display.Rnw’ due to unavailable dependencies:
  'sf'
Note: skipping ‘Ch_missing_values.Rnw’ due to unavailable dependencies:
  'mice'
Note: skipping ‘Ch_multidimensional_scaling.Rnw’ due to unavailable dependencies:
  'ape', 'wordcloud'
Note: skipping ‘Ch_multiple_linear_regression.Rnw’ due to unavailable dependencies:
  'wordcloud'
Note: skipping ‘Ch_simultaneous_inference.Rnw’ due to unavailable dependencies:
  'lme4'
Packages suggested but not available for checking: 'ape', 'lme4'
Note: skipping ‘Ch_analysing_longitudinal_dataI.Rnw’ due to unavailable dependencies:
  'lme4'
Note: skipping ‘Ch_multidimensional_scaling.Rnw’ due to unavailable dependencies:
  'ape'
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 suggested but not available for checking: ‘raster’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hSDM.Rmd’ using rmarkdown

Quitting from lines 61-65 [libraries] (hSDM.Rmd)
Error: processing vignette 'hSDM.Rmd' failed with diagnostics:
there is no package called 'raster'
--- failed re-building ‘hSDM.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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

Package suggested but not available for checking: ‘splm’

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

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

Package suggested but not available for checking: ‘AlphaSimR’

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

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

Package suggested but not available for checking: ‘optmatch’

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

Package suggested but not available for checking: ‘bayesplot’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cld3', 'ranger', 'urltools'

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

Package suggested but not available for checking: ‘qpdf’

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

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

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

Packages suggested but not available for checking:
  'openair', 'editData', 'terra'

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

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

Packages suggested but not available for checking:
  'reshape', 'ggrepel', 'ks'

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 ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = identical(Sys.getenv("TRAVIS"), "true"))
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Specified C++14: please drop specification unless essential
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘spelling’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = nzchar(Sys.getenv("GITHUB_WORKSPACE")))
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package suggested but not available for checking: ‘spelling’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [13s/16s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = identical(Sys.getenv("CI"), "true"))
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages required but not available: 'later', 'promises', 'Rcpp'

Package suggested but not available for checking: ‘websocket’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'httpuv', 'later', 'promises'
Running examples in ‘httr2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: oauth_client_req_auth
> ### Title: OAuth client authentication
> ### Aliases: oauth_client_req_auth oauth_client_req_auth_header
> ###   oauth_client_req_auth_body oauth_client_req_auth_jwt_sig
> 
> ### ** Examples
> 
> # Show what the various forms of client authentication look like
> req <- request("https://example.com/whoami")
> 
> client1 <- oauth_client(
+   id = "12345",
+   secret = "56789",
+   token_url = "https://example.com/oauth/access_token",
+   name = "oauth-example",
+   auth = "body" # the default
+ )
> # calls oauth_client_req_auth_body()
> req_dry_run(oauth_client_req_auth(req, client1))
Error in req_dry_run(oauth_client_req_auth(req, client1)) : 
  The package "httpuv" is required.
Calls: req_dry_run -> check_installed
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘httr2.Rmd’ using rmarkdown

Quitting from lines 50-51 [unnamed-chunk-3] (httr2.Rmd)
Error: processing vignette 'httr2.Rmd' failed with diagnostics:
The package "httpuv" is required.
--- failed re-building ‘httr2.Rmd’

SUMMARY: processing the following file failed:
  ‘httr2.Rmd’

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

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

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

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

Package suggested but not available for checking: ‘inti’

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

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

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

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

Package suggested but not available for checking: ‘spelling’

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

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

Package suggested but not available for checking: ‘qpdf’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘TeXCheckR’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'fst', 'geosphere', 'survey'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'AER', 'devtools', 'flextable', 'ftExtra', 'lme4', 'openxlsx',
  'quarto'
Running examples in ‘huxtable-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_Workbook
> ### Title: Convert a huxtable for Excel
> ### Aliases: as_Workbook as_Workbook.huxtable
> 
> ### ** Examples
> 
> wb <- as_Workbook(jams)
Error in assert_package("as_Workbook", "openxlsx") : 
  `as_Workbook` requires the "openxlsx" package. To install, type:
install.packages("openxlsx")
Calls: as_Workbook -> as_Workbook.huxtable -> assert_package
Execution halted
Packages required but not available:
  'reshape2', 'ggforce', 'Rtsne', 'umap', 'plyr', 'gganimate',
  'markovchain'

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

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

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

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

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

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

Package suggested but not available for checking: ‘microViz’

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: 'forecast', 'nnfor', 'WaveletArima'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'shiny', 'shiny.i18n', 'shinyTime'
Packages required but not available: 'sf', 'terra', 'raster'

Packages suggested but not available for checking:
  'devtools', 'shiny', 'shinyjs', 'shiny.i18n', 'leaflet',
  'leaflet.extras', 'leaflet.esri', 'pangaear'

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

Package suggested but not available for checking: ‘formatdown’

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

Packages suggested but not available for checking:
  'nhdplusTools', 'lwgeom', 'mapview'

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

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

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

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

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

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

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plotly’

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

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

Package suggested but not available for checking: ‘jack’

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

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

Package suggested but not available for checking: ‘webshot2’

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

Packages suggested but not available for checking:
  'Rcpp', 'reshape', 'devtools'

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

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

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

Packages suggested but not available for checking:
  'DT', 'leaflet', 'leaflet.extras', 'mapview', 'plotly', 'sf',
  'shiny', 'shinyalert', 'shinyFiles', 'shinyWidgets'

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

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

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

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

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

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

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

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) IATData.Rd:24: Lost braces; missing escapes or markup?
    24 | Dan Martin {dpmartin42@gmail.com}
       |            ^
Packages required but not available: 'reshape2', 'qgraph'

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

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'ranger', 'reshape2', 'ggrepel', 'GGally', 'DT',
  'gutenbergr', 'tidytext', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ibawds)
  Loading required package: dslabs
  > 
  > test_check("ibawds")
  [ FAIL 1 | WARN 0 | SKIP 9 | PASS 135 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-cran_packages.R:5:3', 'test-cran_packages.R:11:3',
    'test-dist_plots.R:25:3', 'test-dist_plots.R:39:3', 'test-dist_plots.R:55:3',
    'test-dist_plots.R:71:3', 'test-slide_tools.R:37:3', 'test-voronoi.R:8:3'
  • not all the required packages are installed. (1): 'test-install.R:23:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-install.R:91:3'): test get_software_versions() ───────────────
  sw$pkg_installed is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 9 | PASS 135 ]
  Deleting unused snapshots:
  • dist_plots/density-plot-chi2.svg
  • dist_plots/density-plot-poisson.svg
  • dist_plots/density-plot-weibull.svg
  • dist_plots/distribution-plot-poisson-continuous.svg
  • dist_plots/distribution-plot-uniform.svg
  • voronoi/voronoi-suppress-data.svg
  • voronoi/voronoi-uncoloured-data.svg
  • voronoi/voronoi-with-data.svg
  • voronoi/voronoi-with-options.svg
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

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

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

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
Package required but not available: ‘Rcpp’

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

Packages suggested but not available for checking:
  'RcppArmadillo', 'magick', 'gganimate'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ranger’
checkRd: (-1) setServerLogLevel.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) setServerLogLevel.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) betaS1lr.Rd:28: Lost braces; missing escapes or markup?
    28 |  \item{Rm1U}{matrix R^{-1}U (see reference).}
       |                       ^
checkRd: (-1) lrsmoother.Rd:32: Lost braces; missing escapes or markup?
    32 |   R^{-1}U (see reference) and \link{smoothCon} for the definition of smoothobject}
       |     ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'reshape2', 'mc2d'

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', 'icenReg', 'RcppArmadillo'

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

Package suggested but not available for checking: ‘RLRsim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
'LazyData' is specified without a 'data' directory
Running examples in ‘ICCbin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iccbin
> ### Title: Estimates Intracluster Correlation coefficients (ICC) and it's
> ###   confidence intervals (CI)
> ### Aliases: iccbin
> 
> ### ** Examples
> 
> bccdata <- rcbin(prop = .4, prvar = .2, noc = 30, csize = 20, csvar = .2, rho = .2)
> iccbin(cid = cid, y = y, data = bccdata)
Warning in iccbin(cid = cid, y = y, data = bccdata) :
  One or Both of 'Zou and Donner's Modified Wald' Confidence Limits Fell Outside of [0, 1]
Error: Package 'lme4' is needed for methods 'lin' and 'sim'. Please install it.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmmTMB’

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

Package suggested but not available for checking: ‘LTRCtrees’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Packages required but not available:
  'plotly', 'Rtsne', 'ggrepel', 'ggpubr', 'shiny', 'ape', 'plyr',
  'reshape', 'uwot', 'Rcpp'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mixAK', 'icenReg', 'frailtypack', 'cubature', 'dynsurv'
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:
  'shiny', 'shinythemes', 'DT', 'ggrepel', 'shinyhelper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Bpa.Rd:39-40: Lost braces
    39 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) Fpa.Rd:42-43: Lost braces
    42 | stocks. \doi{10.17895/ices.pub.3036}{\emph{ICES Advice
       |                                     ^
checkRd: (-1) icesRound.Rd:64-65: Lost braces
    64 | \doi{10.17895/ices.pub.3038}{\emph{ICES Advice Technical
       |                             ^
checkRd: (-1) mohn.Rd:71-72: Lost braces
    71 | \doi{10.17895/ices.pub.5997}{\emph{ICES Scientific Reports
       |                             ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'sf', 'lwgeom', 'units', 'leaflet', 'leafgl', 'leaflet.extras',
  'leafsync', 'miniUI', 'shiny', 'rnaturalearth'

Packages suggested but not available for checking:
  'DT', 'mapview', 'reshape2', 'plotly', 'CopernicusDEM', 'terra'

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: 'RcppSimdJson', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘relaimpo’
Note: skipping ‘ic.infer.rnw’ due to unavailable dependencies: 'relaimpo'
Packages required but not available:
  'rugarch', 'car', 'coefplot', 'forecast', 'openair', 'papeR'

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

Package suggested but not available for checking: ‘survminer’

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

Package suggested but not available for checking: ‘icenReg’

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

Package suggested but not available for checking: ‘forecast’

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

Package suggested but not available for checking: ‘terra’

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

Packages suggested but not available for checking: 'flexsurv', 'lemon'

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘ICSClust’

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

Packages suggested but not available for checking: 'ICSNP', 'ICSOutlier'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) data.Rd:7: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) data.Rd:9: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘minqa’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ICS', 'Rcpp', 'ICSNP', 'survey', 'GGally', 'RcppRoll',
  'RcppArmadillo'

Package suggested but not available for checking: ‘fICA’

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

Package suggested but not available for checking: ‘metR’

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: 'FD', 'picante', 'ape'

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

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nrba', 'shiny', 'flexdashboard', 'shinyjs', 'DT', 'survey', 'srvyr',
  'openxlsx', 'miniUI'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggimage', 'pdftools', 'ggpubr', 'ggtext', 'shiny', 'openxlsx'

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

Package suggested but not available for checking: ‘bayesm’

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

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

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

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: ‘RcppRoll’

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

Packages suggested but not available for checking:
  'ggpubr', 'ggtree', 'phytools', 'treeio', 'shiny', 'shinydashboard',
  'rclipboard', 'shinyjs'

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

Package suggested but not available for checking: ‘readtext’

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

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

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

Quitting from lines 25-32 [unnamed-chunk-2] (model_details.Rmd)
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘model_details.Rmd’

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

Quitting from lines 24-31 [unnamed-chunk-2] (parameter_details.Rmd)
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘parameter_details.Rmd’

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

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

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

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', '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.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘GA’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'sf', 'spelling'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Southeast-USA-Engineering-Weather-Map.Rmd’ using rmarkdown

Quitting from lines 23-95 [unnamed-chunk-1] (Southeast-USA-Engineering-Weather-Map.Rmd)
Error: processing vignette 'Southeast-USA-Engineering-Weather-Map.Rmd' failed with diagnostics:
could not find function "st_as_sf"
--- failed re-building ‘Southeast-USA-Engineering-Weather-Map.Rmd’

--- re-building ‘USA-Engineering-Weather-Map.Rmd’ using rmarkdown

Quitting from lines 23-93 [unnamed-chunk-1] (USA-Engineering-Weather-Map.Rmd)
Error: processing vignette 'USA-Engineering-Weather-Map.Rmd' failed with diagnostics:
could not find function "st_as_sf"
--- failed re-building ‘USA-Engineering-Weather-Map.Rmd’

SUMMARY: processing the following files failed:
  ‘Southeast-USA-Engineering-Weather-Map.Rmd’
  ‘USA-Engineering-Weather-Map.Rmd’

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

Package suggested but not available for checking: ‘spelling’

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

Packages suggested but not available for checking:
  'reticulate', 'rpymat', 'RNifti'

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

Quitting from lines 23-142 [unnamed-chunk-1] (Analysis-using-tm-vignette.Rmd)
Error: processing vignette 'Analysis-using-tm-vignette.Rmd' failed with diagnostics:
could not find function "DocumentTermMatrix"
--- failed re-building ‘Analysis-using-tm-vignette.Rmd’

--- re-building ‘View-PDFs-vignette.Rmd’ using rmarkdown
--- finished re-building ‘View-PDFs-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Analysis-using-tm-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'shiny', 'reshape2', 'rpf', 'OpenMx'

Package suggested but not available for checking: ‘plyr’

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

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

Packages suggested but not available for checking:
  'IFCdata', 'shiny', 'reticulate'

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Found the following assignments to the global environment:
File ‘IgorR/R/ReadIgorBinary.R’:
  assign(WaveName, rval, envir = .GlobalEnv)
Packages required but not available:
  'shiny', 'shinydashboard', 'shinyWidgets', 'shinyFiles', 'sortable',
  'fuzzyjoin', 'fst', 'feather', 'mapsf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ape’
Skipping checking math rendering: package 'V8' unavailable
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking: 'metR', 'rnaturalearth'
Error(s) in re-building vignettes:
  ...
--- re-building ‘igrf.Rmd’ using rmarkdown

Quitting from lines 55-85 [unnamed-chunk-3] (igrf.Rmd)
Error: processing vignette 'igrf.Rmd' failed with diagnostics:
there is no package called 'metR'
--- failed re-building ‘igrf.Rmd’

SUMMARY: processing the following file failed:
  ‘igrf.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘sf’

Packages suggested but not available for checking: 'tmap', 'units'

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 suggested but not available for checking: 'shiny', 'reshape2'
Packages required but not available:
  'xaringan', 'pdftools', 'servr', 'tidytext', 'bib2df', 'pagedown'

Packages suggested but not available for checking: 'DT', 'leaflet', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'MTPS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘brms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fda.usc’

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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'magick'

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.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'magick', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘magick’

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: 'dae', 'GGally', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magick', 'OpenImageR'

Package suggested but not available for checking: ‘shiny’

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.
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.
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: 'imager', 'Rcpp'

Package suggested but not available for checking: ‘tesseract’

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', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'keras', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'magick'

Package suggested but not available for checking: ‘opencv’

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 required but not available: 'caret', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rcccd', 'Rfast', 'SMOTEWB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'KernelKnn', 'Rcpp', 'smotefamily', 'C50', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RNifti'

Package suggested but not available for checking: ‘mmand’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IsingSampler', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'MBESS'

Package suggested but not available for checking: ‘mediation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘magick’
Package suggested but not available for checking: ‘magick’
Package required but not available: ‘reshape2’

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.
Package required but not available: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'glmnet', 'keras', 'ranger'
Running examples in ‘iml-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LocalModel
> ### Title: LocalModel
> ### Aliases: LocalModel
> 
> ### ** Examples
> 
> library("randomForest")
randomForest 4.7-1.2
Type rfNews() to see new features/changes/bug fixes.
> # First we fit a machine learning model on the Boston housing data
> data("Boston", package = "MASS")
> X <- Boston[-which(names(Boston) == "medv")]
> rf <- randomForest(medv ~ ., data = Boston, ntree = 50)
> mod <- Predictor$new(rf, data = X)
> 
> # Explain the first instance of the dataset with the LocalModel method:
> x.interest <- X[1, ]
> lemon <- LocalModel$new(mod, x.interest = x.interest, k = 2)
Loading required package: glmnet
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glmnet’
Error in initialize(...) : Please install glmnet.
Calls: <Anonymous> -> initialize
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'clusterProfiler', 'DOSE', 'openxlsx', 'proxyC', 'ggheatmap',
  'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CDM', 'Rcpp', 'sirt', 'TAM', 'RcppArmadillo'

Package which this enhances but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'pROC'

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:
  'factoextra', 'UpSetR', 'ggrepel', 'reshape2', 'Rtsne', 'shiny',
  'shinythemes', 'Rcpp', 'ggpubr', 'plyr', 'ape', 'phangorn', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'caret', 'pROC', 'Rtsne', 'dbscan', 'clusterSim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape2', 'repmis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'missMDA', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'parallelDist', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘accdata’

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: 'tableHTML', 'spelling'
Package suggested but not available for checking: ‘odbc’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'shiny', 'shinyBS', 'shinythemes', 'compareGroups'
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tolerance’

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: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom-imprinting-types.Rmd’ using rmarkdown
--- finished re-building ‘custom-imprinting-types.Rmd’

--- re-building ‘intro-to-imprinting.Rmd’ using rmarkdown

Quitting from lines 38-39 [unnamed-chunk-3] (intro-to-imprinting.Rmd)
Error: processing vignette 'intro-to-imprinting.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘intro-to-imprinting.Rmd’

SUMMARY: processing the following file failed:
  ‘intro-to-imprinting.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'caret', 'glmnet', 'Cubist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'imputeTS', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggtext', 'forecast', 'Rcpp'

Package suggested but not available for checking: ‘tsibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bayesplot', 'caret', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘extRemes’

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.
Skipping checking math rendering: package 'V8' unavailable
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Package suggested but not available for checking: ‘survey’

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:
  'dtwclust', 'parallelDist', 'rucrdtw', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ciTools’
Note: skipping ‘incidence2.Rmd’ due to unavailable dependencies: 'ciTools'
Packages suggested but not available for checking:
  'odbc', 'spelling', 'gt', 'flextable'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘backbone’
checkRd: (-1) make_likelihood_matrix.Rd:16: Lost braces; missing escapes or markup?
    16 | This function creates a matrix such that P[t, s] = P(C = t | I = s) = theta_{t-s} for s <= t and 0 otherwise.
       |                                                                             ^
Packages required but not available: 'cubature', 'plyr'

Package suggested but not available for checking: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ape', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘osqp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RcppBDT’

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: ‘FactoMineR’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gfonts’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘SixSigma’

Packages suggested but not available for checking:
  'learnr', 'car', 'ggforce', 'ggraph', 'RcmdrMisc', 'gt', 'ggtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'tibbletime'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'hdi', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'tidytree', 'phyclust', 'ape', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggpubr', 'iNEXT.3D'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'iNEXT.3D', 'tidytree', 'phyclust', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggnetwork', 'ggraph', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'gganimate', 'ggExtra', 'ggpubr', 'plotly', 'precrec', 'pROC',
  'Rtsne', 'RTransferEntropy', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘xplorerr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘minfi’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

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:
  'NNS', 'shiny', 'shinythemes', 'shinyWidgets', 'shinyjs',
  'shinycssloaders', 'colourpicker', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nanotime', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'mapSpain', 'preferably'
Running examples in ‘infoelectoral-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: candidatos
> ### Title: Download candidate data
> ### Aliases: candidatos
> 
> ### ** Examples
> 
> data <- candidatos(
+   tipo_eleccion = "senado", anno = "2004",
+   mes = "03", nivel = "municipio"
+ )
Downloading https://infoelectoral.interior.gob.es/estaticos/docxl/apliextr/03200403_MUNI.zip
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL peer certificate or SSH remote key was not OK: [infoelectoral.interior.gob.es] server verification failed: certificate signer not trusted. (CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none)
Calls: candidatos ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gMCP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘gurobi’
Package required but not available: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fields’

Package suggested but not available for checking: ‘rNOMADS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spaMM', 'blackbox', 'ranger', 'geometry'

Packages suggested but not available for checking:
  'Rmixmod', 'caret', 'xLLiM', 'reticulate', 'mafR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ranger’
Running examples in ‘ingredients-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aggregate_profiles
> ### Title: Aggregates Ceteris Paribus Profiles
> ### Aliases: aggregate_profiles
> 
> ### ** Examples
> 
> library("DALEX")
Welcome to DALEX (version: 2.4.3).
Find examples and detailed introduction at: http://ema.drwhy.ai/
Additional features will be available after installation of: ggpubr.
Use 'install_dependencies()' to get all suggested dependencies

Attaching package: ‘DALEX’

The following object is masked from ‘package:ingredients’:

    feature_importance

> library("ingredients")
> library("ranger")
Error in library("ranger") : there is no package called ‘ranger’
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DALEX)
  Welcome to DALEX (version: 2.4.3).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  > library(ingredients)
  
  Attaching package: 'ingredients'
  
  The following object is masked from 'package:DALEX':
  
      feature_importance
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("ingredients")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ingredients.Rcheck/tests/testthat/helper-objects.R"
  Caused by error in `library()`:
  ! there is no package called 'ranger'
  Backtrace:
       ▆
    1. ├─testthat::test_check("ingredients")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("ranger") at tests/testthat/helper-objects.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘metR’

Packages suggested but not available for checking:
  'spelling', 'survminer', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spdep’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fmesher', 'plyr', 'sf', 'terra'

Packages suggested but not available for checking:
  'ggmap', 'INLA', 'raster', 'shiny', 'tidyterra'

Package which this enhances but not available for checking: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'INLA', 'JMbayes2', 'rstanarm', 'frailtypack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'INLA', 'spelling'
Packages required but not available: 'fmesher', 'sf', 'terra'

Packages suggested but not available for checking:
  'INLA', 'inlabru', 'rnaturalearth'

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:
  'DiagrammeRsvg', 'V8', 'webmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcpp’
Package required but not available: ‘tm’

Packages suggested but not available for checking:
  'chromote', 'magick', 'pdftools', 'tesseract', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

Packages suggested but not available for checking:
  'fastshap', 'GGally', 'keras', 'lime', 'luz', 'plotly', 'ranger',
  'spelling', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'wordcloud', 'tm', 'entropart'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'ggpubr', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'aphid', 'kmer', 'phylogram', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFactor', 'bife', 'blavaan', 'blme', 'brms',
  'car', 'censReg', 'cgam', 'cplm', 'crch', 'epiR', 'estimatr',
  'feisr', 'fixest', 'fungible', 'gamm4', 'glmmTMB', 'glmtoolbox',
  'gt', 'interp', 'ivreg', 'lavaSearch2', 'lme4', 'lmerTest',
  'logistf', 'marginaleffects', 'MCMCglmm', 'merTools', 'metaBMA',
  'metaplus', 'mice', 'mmrm', 'multgee', 'nestedLogit', 'panelr',
  'pbkrtest', 'plm', 'PROreg', 'Rcpp', 'RcppEigen', 'robustlmm',
  'rstanarm', 'rstantools', 'survey', 'svylme', 'TMB'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘RSpectra’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggfittext', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'brms', 'DT', 'lme4', 'pander', 'plotly', 'shiny', 'shinyalert',
  'shinyFeedback', 'shinyjs', 'shinytoastr', 'shinyvalidate',
  'tidybayes', 'tippy', 'waiter'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking: 'devtools', 'plyr'
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |             ^
checkRd: (-1) ask.user.yn.question.Rd:44: Lost braces; missing escapes or markup?
    44 | menu in the {utils} package, yesno in the {devtools} package.
       |                                           ^
checkRd: (-1) install.FFmpeg.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is useful for saveVideo() in the {animation} package.
       |                                                ^
checkRd: (-1) install.SWFTools.Rd:27: Lost braces; missing escapes or markup?
    27 | This function is useful for saveSWF() in the {animation} package.
       |                                              ^
checkRd: (-1) os.shutdown.Rd:25: Lost braces; missing escapes or markup?
    25 | This function is a modified version of Yihui's shutdown function from the {fun} package.
       |                                                                           ^
Malformed Title field: should not end in a period.
Packages required but not available: 'ciTools', 'DHARMa'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'intamap', 'automap', 'gstat', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'sf', 'automap'

Package suggested but not available for checking: ‘psgp’

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: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'MultivariateRandomForest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DiagrammeRsvg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pointblank’
Package suggested but not available for checking: ‘vcr’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(intensegRid)
  > 
  > test_check("intensegRid")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/intensegRid.Rcheck/tests/testthat/setup-intensegRid.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("intensegRid")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-intensegRid.R:1:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Package required but not available: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘chngpt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'flextable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘jtools’

Packages suggested but not available for checking: 'lme4', 'survey'

Packages which this enhances but not available for checking:
  'brms', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'shiny', 'shinyFeedback', 'waiter', 'ggrepel', 'openxlsx',
  'shinyWidgets', 'FactoMineR', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'DescTools', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'spelling'
Packages required but not available:
  'Lmoments', 'pROC', 'ModelMetrics', 'Rcpp', 'AER', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyBS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'geometries'

Package suggested but not available for checking: ‘sfheaders’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'simplextree', 'reticulate'

Package suggested but not available for checking: ‘TDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppCGAL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: ‘Ryacas’

Package which this enhances but not available for checking: ‘RcppEigen’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘Rdisop’

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.
Packages required but not available: 'fixest', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) interval-internal.Rd:40: Lost braces
    40 | \item{dqfunc}{function, density of the results of the quantile function, e.g., function(x){dnorm(qnorm(x))} (used for 'general' scores, 
       |                                                                                           ^
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:
  'clinUtils', 'flextable', 'ggrepel', 'plyr', 'reshape2'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'lme4', 'FactoMineR', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gstat', 'raster', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NMF', 'InterSIM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'reshape2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'terra', 'sf', 'PointedSDMs', 'geodata', 'inlabru', 'giscoR',
  'blockCV', 'rgbif', 'tidyterra'

Packages suggested but not available for checking: 'INLA', 'lwgeom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Inventorymodel-package.Rd:34: Lost braces
    34 | M.G. Fiestras-Janeiro, I. García-Jurado, A. Meca, M.A. Mosquera (2015). Cooperation on capacitated inventory situations with fixed holding costs. emph{European Journal of Operational Research}, \bold{241}(3), 719--726.
       |                                                                                                                                                       ^
Package required but not available: ‘sparseLRMatrix’

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: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘iNZightPlots’
Packages required but not available: 'iNZightTools', 'units', 'survey'

Packages suggested but not available for checking:
  'ggmosaic', 'ggtext', 'plotly', 'waffle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'GGally', 'ggrepel', 'ggtext', 'iNZightPlots'

Packages suggested but not available for checking: 'iNZightTools', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'srvyr', 'survey', 'units'

Packages suggested but not available for checking: 'surveyspec', 'tsibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggtext', 'tsibble', 'fable', 'fabletools', 'feasts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) f.influence.Rd:25: Lost braces; missing escapes or markup?
    25 | where F is the field of influence, k is order of influence, l_{ij} is the ith row and jth column element of the Leontief Inverse and -s indicates the sth element has been removed.
       |                                                               ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plotly', 'shiny', 'reshape2', 'Rcpp'

Packages suggested but not available for checking:
  'Rcpp', 'shinyjs', 'colourpicker', 'DT', 'shinydashboard',
  'RVCompare', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'matlib', 'randomcoloR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) aiPux.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPux.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aiPuxComposite.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dls2007.Rd:19: Lost braces
    19 | impact. emph{Journal of Applied Psychology}, 92(5), 1380.
       |             ^
checkRd: (-1) paretoXX.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXX.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) paretoXY.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'eurostat', '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: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’, ‘Rf_StringFalse’, ‘Rf_StringTrue’,
    ‘Rf_isBlankString’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘fuzzyjoin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'treemap', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'KRIS', 'apcluster', 'Rmixmod'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘promises’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'ranger'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gdistance', 'sf', 'raster'

Package suggested but not available for checking: ‘gstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'geobr', 'reshape', 'sf'
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_ipeaplot.Rmd’ using rmarkdown

Quitting from lines 64-74 [unnamed-chunk-3] (intro_ipeaplot.Rmd)
Error: processing vignette 'intro_ipeaplot.Rmd' failed with diagnostics:
there is no package called 'geobr'
--- failed re-building ‘intro_ipeaplot.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_ipeaplot.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'apcluster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sommer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'lme4', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘growthrates’
Running examples in ‘ipolygrowth-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ipg_multisample
> ### Title: Growth parameter estimates for multiple samples
> ### Aliases: ipg_multisample
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> data <- growthrates::bactgrowth
Error in loadNamespace(x) : there is no package called ‘growthrates’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘prodlim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'reshape2', 'RcppEigen'

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'secr', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phangorn', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘extraDistr’

Packages suggested but not available for checking: 'GGally', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hipread’

Packages suggested but not available for checking:
  'DT', 'rmapshaper', 'sf', 'shiny', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mice’
Running examples in ‘IPWboxplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IPW.ASYM.boxplot
> ### Title: Boxplot adapted to skewness and missing values
> ### Aliases: IPW.ASYM.boxplot
> ### Keywords: quantile boxplot missing inverse probability weighted
> 
> ### ** Examples
> 
> 
> ## A real data example
> 
> 
> library(mice)
Error in library(mice) : there is no package called ‘mice’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘survey’
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'ggforce', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘mpath’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'GGMncv'

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: 'imager', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'twang', 'survey', 'rstanarm', 'RSelenium', 'DisImpact', 'sf',
  'tigris', 'tidycensus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppRoll’

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: 'IRISSeismic', 'seismicRoll'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘seismicRoll’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) partial_eigen.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) partial_eigen.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:41-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:47-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prcomp_irlba.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ssvd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'ggpubr'

Package suggested but not available for checking: ‘reshape’

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) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
Packages required but not available: 'ChemoSpec', 'hyperSpec', 'units'

Packages suggested but not available for checking: 'fda', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MEMSS’
Running examples in ‘IrregLong-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: abacus.plot
> ### Title: Create an abacus plot Creates an abacus plot, depicting visits
> ###   per subject over time
> ### Aliases: abacus.plot
> 
> ### ** Examples
> 
> library(MEMSS)
Error in library(MEMSS) : there is no package called ‘MEMSS’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Irreglong-vignette.Rmd’ using rmarkdown

Quitting from lines 58-63 [unnamed-chunk-1] (Irreglong-vignette.Rmd)
Error: processing vignette 'Irreglong-vignette.Rmd' failed with diagnostics:
there is no package called 'MEMSS'
--- failed re-building ‘Irreglong-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Irreglong-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘plyr’
Running examples in ‘irrICC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ci.ICC1a
> ### Title: Confidence Interval of Intraclass Correlation Coefficient (ICC)
> ###   under ANOVA Model 1A.
> ### Aliases: ci.ICC1a
> 
> ### ** Examples
> 
> #iccdata3 is a small dataset that comes with the package. Use it as follows:
> library(irrICC)
> iccdata3 #see what the iccdata3 dataset looks like
  Subject Rater1 Rater2 Rater3
1       1     12     18     NA
2       2     14     12     13
3       3     19     17     21
4       4     24     30     NA
> ci.ICC1a(iccdata3)
Error in loadNamespace(x) : there is no package called ‘plyr’
Calls: ci.ICC1a ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PrecisionMeasures.Rmd’ using rmarkdown

Quitting from lines 25-37 (PrecisionMeasures.Rmd)
Error: processing vignette 'PrecisionMeasures.Rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘PrecisionMeasures.Rmd’

--- re-building ‘UserGuide.Rmd’ using rmarkdown

Quitting from lines 51-52 [unnamed-chunk-3] (UserGuide.Rmd)
Error: processing vignette 'UserGuide.Rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘UserGuide.Rmd’

SUMMARY: processing the following files failed:
  ‘PrecisionMeasures.Rmd’ ‘UserGuide.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'DT', 'mirt', 'shiny', 'shinyWidgets', 'shinycssloaders', 'bs4Dash',
  'gt', 'mirtCAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dcurver’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinycssloaders', 'mirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'Rfast', '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 suggested but not available for checking:
  'lme4', 'mirt', 'flextable', 'reshape2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘pretree_vignette.Rmd’ using rmarkdown

Quitting from lines 15-23 [setup] (pretree_vignette.Rmd)
Error: processing vignette 'pretree_vignette.Rmd' failed with diagnostics:
there is no package called 'flextable'
--- failed re-building ‘pretree_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘pretree_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'mirt', 'fastGHQuad'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyAce'

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: ‘xcms’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘labourR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) analyseISE.Rd:66: Lost braces; missing escapes or markup?
    66 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) analyseISE.Rd:69: Lost braces; missing escapes or markup?
    69 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
checkRd: (-1) describeISE.Rd:71: Lost braces; missing escapes or markup?
    71 |         False positive rate used for detection threshold (not output) to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                                                     ^
checkRd: (-1) describeISE.Rd:74: Lost braces; missing escapes or markup?
    74 |         False negative rate used to calculate LOD(alpha, beta) {only returned if SN = NA}
       |                                                                ^
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'glmnet'

Package suggested but not available for checking: ‘IsingSampler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gganimate', 'plotly', 'shiny', 'shinycssloaders', 'shinythemes',
  'simlandr'

Packages suggested but not available for checking:
  'IsingFit', 'IsingSampler', 'transformr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'magick', 'sf'
Specified C++11: please drop specification unless essential
Packages required but not available: 'ggrepel', 'qgraph', 'reshape2'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'plyr'

Package suggested but not available for checking: ‘rasterVis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |     ^
checkRd: (-1) CLM.Rd:30: Lost braces
    30 | item{tau0}{the mean circular Kendall Tau of the initial order with the data.}
       |           ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'DT', 'golem', 'plyr', 'shiny', 'shinyalert', 'shinyjs'

Package suggested but not available for checking: ‘shinytest2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'osqp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘openxlsx’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'interp', 'tinysnapshot'
Running examples in ‘isopleuros-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ternary_contour
> ### Title: Contour Lines
> ### Aliases: ternary_contour ternary_contour-method
> ###   ternary_contour,numeric,numeric,numeric-method
> ###   ternary_contour,ANY,missing,missing-method
> 
> ### ** Examples
> 
> ## Add density
> ## Data from Aitchison 1986
> ternary_plot(arctic, panel.first = ternary_grid())
> levels <- ternary_contour(arctic, value = arctic$depth, n = 100, nlevels = 10)
Error: The interp package is required. Please install it.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shinylight’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'latticeExtra', 'rasterVis', 'spaMM', 'terra'

Packages suggested but not available for checking:
  'elevatr', 'magick', 'spelling', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘coneproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'bayesplot', 'ggdist', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘outliertree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'openxlsx', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ibd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'rnaturalearth', 'sf'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'datamods', 'DT', 'openxlsx', 'rsdmx', 'shiny', 'shinyBS',
  'shinydashboard', 'shinyhelper', 'shinyjs', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyBS', 'shinyWidgets', 'shiny', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'keras', 'tensorflow', 'philentropy'

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape’

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: ‘energy’

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: 'einsum', 'mixOmics'

Package suggested but not available for checking: ‘nnTensor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Cyclops’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reticulate’
Running examples in ‘iterors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: r_to_py.iteror
> ### Title: Wrap an iteror to appear as a Python iterator or vice versa.
> ### Aliases: r_to_py.iteror iteror.python.builtin.object
> 
> ### ** Examples
> 
> pit <- reticulate::r_to_py(iseq(2, 11, 5))
Error in loadNamespace(x) : there is no package called ‘reticulate’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.r’ [36s/44s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  > library(iterors)
  > 
  > test_check("iterors")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 2190 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-py.R:2:3'): Iteror from Python object ──────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'reticulate'
  Backtrace:
      ▆
   1. ├─iterors:::skip_if_no_python() at test-py.R:2:3
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-py.R:12:3'): Python object from iteror ─────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'reticulate'
  Backtrace:
      ▆
   1. ├─iterors:::skip_if_no_python() at test-py.R:12:3
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-py.R:24:3'): round trip both ways ──────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'reticulate'
  Backtrace:
      ▆
   1. ├─iterors:::skip_if_no_python() at test-py.R:24:3
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 2190 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'plyr', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'seqinr', 'ape', 'miniUI', 'shiny', 'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'NMF', 'pcalg'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 45-47 [unnamed-chunk-3] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'NMF'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rcbalance’

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: 'compositions', 'ggcorrplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'car', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fastshap', 'isotree', 'outliertree', 'raster', 'sf', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BSSprep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
Packages required but not available: 'fixest', 'wCorr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ivreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘locClass’
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gurobi', 'cplexAPI', 'splines2', 'pander', 'AER'
checkRd: (-1) sTsls.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{pi}{the matrix E[XZ']E[ZZ']^{-1}}
       |                                   ^
checkRd: (-1) sTslsSplines.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{pi}{matrix, corresponds to E[XZ']E[ZZ']^{-1}, the first stage
       |                                               ^
Running examples in ‘ivmte-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: uSplineBasis
> ### Title: Spline basis function
> ### Aliases: uSplineBasis
> 
> ### ** Examples
> 
> ## Since the splines are declared as part of the MTR, you will need
> ## to have parsed out the spline command. Thus, this command will be
> ## called via eval(parse(text = .)). In the examples below, the
> ## commands are parsed from the object \code{splineslist} generated
> ## by \code{\link[MST]{removeSplines}}. The names of the elements in
> ## the list are the spline commands, and the elements themselves are
> ## the terms that interact with the splines.
> 
> ## Declare MTR function
> m0 = ~ x1 + x1 : uSpline(degree = 2,
+                           knots = c(0.2, 0.4)) +
+     x2 : uSpline(degree = 2,
+                   knots = c(0.2, 0.4)) +
+     x1 : x2 : uSpline(degree = 2,
+                        knots = c(0.2, 0.4)) +
+     uSpline(degree = 3,
+              knots = c(0.2, 0.4),
+              intercept = FALSE)
> 
> ## Extract spline functions from MTR function
> splineslist <- removeSplines(m0)$splineslist
> 
> ## Declare points at which we wish to evaluate the spline functions
> x <- seq(0, 1, 0.2)
> 
> ## Evaluate the splines
> eval(parse(text = gsub("uSpline\\(",
+                        "ivmte:::uSplineBasis(x = x, ",
+                         names(splineslist)[1])))
Error in loadNamespace(x) : there is no package called ‘splines2’
Calls: eval ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ivmte)
  > 
  > test_check("ivmte")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 22 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_splines.R:8:1'): (code run outside of `test_that()`) ───────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'splines2'
  Backtrace:
      ▆
   1. ├─ivmte:::gendistSplines() at test_splines.R:8:1
   2. │ ├─base::t(...)
   3. │ └─base::sapply(...)
   4. │   └─base::lapply(X = X, FUN = FUN, ...)
   5. │     └─ivmte (local) FUN(X[[i]], ...)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base (local) withOneRestart(expr, restarts[[1L]])
   9.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 22 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Packages suggested but not available for checking: 'AER', 'effects', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

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: 'forecast', '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: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'gitear', 'miniUI', 'shiny.i18n', 'shiny', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘coala’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'tm', 'anytime', 'cffr'
Packages required but not available: 'Rcpp', 'qvalue'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'coala', 'scrm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qspray', 'ratioOfQsprays', 'symbolicQspray', 'DescTools',
  'multicool', 'mvp', 'RationalMatrix', 'Rcpp', 'spray', 'RcppCGAL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Benchmarking', 'reshape', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ClusterR', 'genio'

Packages suggested but not available for checking:
  'qvalue', 'lfa', 'gcatest'

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: 'Carlson', 'Rcpp', 'Rvcg'

Package suggested but not available for checking: ‘RcppColors’

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: 'ICS', 'ICSNP'
Running examples in ‘JADE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multscatter
> ### Title: Function to Compute Several Scatter Matrices for the Same Data
> ### Aliases: multscatter
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> # example requires the packages ICS and ICSNP
> library(ICSNP)
Error in library(ICSNP) : there is no package called ‘ICSNP’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fst', 'qs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
Packages required but not available:
  'keras', 'tensorflow', 'narray', 'StatRank', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggExtra', 'GGally', 'qpdf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘GA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rworldmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'narray', 'imputeTS', 'philentropy', 'greybox', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SMUT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bde', 'extraDistr', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen',
  'StanHeaders'

Packages suggested but not available for checking:
  'fairness', 'samplingbook'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'dynlm', 'openxlsx'
Running examples in ‘JFE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: durbinH
> ### Title: calculate Sortino Ratio of performance over downside risk
> ### Aliases: durbinH
> 
> ### ** Examples
> 
> 
>   data(macrodata)
>   y=ts(macrodata[,"OECD"],start=c(1961,1),freq=12) #OECD business cycle index
> 
>  out1=dynlm::dynlm(y~L(y,1)+season(y)+trend(y))
Error in loadNamespace(x) : there is no package called ‘dynlm’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'Rvcg', 'randomcoloR', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘jiebaR’
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                        ^
checkRd: (-1) jointLPM.Rd:298: Lost braces; missing escapes or markup?
   298 | following transformation b_1 + b_2*I_1(Y(t)) + ... + b_{n+2}*I_{n+1}(Y(t)),
       |                                                                ^
checkRd: (-1) jointLPM.Rd:299: Lost braces; missing escapes or markup?
   299 | where I_1,...,I_{n+1} is the basis of quadratic I-splines. To constraint the
       |                 ^
Packages required but not available: 'sf', 'units'

Package suggested but not available for checking: ‘lwgeom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'Rcpp', 'shiny', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'JMbayes2', 'joineRML', 'rstanarm', 'FastJM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'roptim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                          ^
checkRd: (-1) jmdem.control.Rd:42: Lost braces; missing escapes or markup?
    42 |     The control argument of \code{jmdem} is by default passed to the control argument of {jmdem.fit}, which uses its elements as arguments to {jmdem.control}: the latter provides defaults and sanity checking.
       |                                                                                                                                               ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'caret', 'timeROC', 'RcppEigen'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RProtoBuf’
Packages required but not available:
  'car', 'GGally', 'BayesFactor', 'afex', 'ggrepel'

Package suggested but not available for checking: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'jmv', 'RProtoBuf'
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘bindrcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'palasso', 'cornet'

Packages suggested but not available for checking:
  'mice', 'remMap', 'MultivariateRandomForest', 'mcen', 'GPM', 'MTPS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mcmcse’

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rstpm2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggrepel’

Packages suggested but not available for checking:
  'devtools', 'MatchIt', 'optmatch', 'optweight'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openxlsx', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘mitml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SpATS', 'fds', 'fields', 'spam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘onion’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [2s/3s]
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
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'rclipboard', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘collapse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stars', 'sf', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leaflet', 'miniUI', 'sf', 'shiny', 'units'

Package suggested but not available for checking: ‘lwgeom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'umap', 'factoextra', 'scran', 'RcppArmadillo'

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppGSL'

Packages suggested but not available for checking:
  'terra', 'boral', 'Hmsc', 'BayesComm', 'ape', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'molaR', 'Rvcg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mediation’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'DT', 'flextable', 'GGally', 'ggpubr', 'jskm', 'jstable', 'MatchIt',
  'pROC', 'rvg', 'shiny', 'shinycustomloader', 'shinyjs',
  'shinyWidgets', 'survey', 'timeROC', 'ggrepel'

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘V8’

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: ‘sf’
Package required but not available: ‘V8’

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: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'tableone', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'chromote', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'miniUI', 'shiny', 'shinyAce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'mniw', 'reshape2'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'sparta', 'RcppArmadillo'

Package suggested but not available for checking: ‘ess’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pander’

Packages suggested but not available for checking:
  'lme4', 'lmerTest', 'pbkrtest', 'survey', 'weights'

Packages which this enhances but not available for checking:
  'brms', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘juicyjuice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DiagrammeRsvg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BayesFactor', 'shiny', 'Superpower', 'shinydashboard', 'qpdf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'mice', 'lme4', 'fst'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'magick', 'webshot2'
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘extraDistr’

Package suggested but not available for checking: ‘tinysnapshot’

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', 'plyr'

Package suggested but not available for checking: ‘clustMD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bigmemory’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'transport', 'Rcpp'

Package suggested but not available for checking: ‘kanjistat.data’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘shiny’

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: ‘aRtsy’
Running examples in ‘KaradaColor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kg_get_color
> ### Title: Get color palette data
> ### Aliases: kg_get_color kg_get_palette
> 
> ### ** Examples
> 
> library("scales")
> show_col(kg_get_color(n = 20, name = "Totan", alpha = 0.5))
> 
> library("aRtsy")
Error in library("aRtsy") : there is no package called ‘aRtsy’
Execution halted
Package required but not available: ‘gganimate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) get.fit.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:57-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get.fit.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.fit.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get.sim.trajectories.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'MVN', 'stlplus', 'forecast', 'nonlinearTseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dbscan', 'umap'

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.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RSpectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Ckmeans.1d.dp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'roll', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘univariateML’

Package suggested but not available for checking: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'cctools', 'kdecopula'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'extraDistr', 'Rfast'

Packages suggested but not available for checking:
  'plotly', 'spdep', 'sf', 'geobr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) kdist.Rd:14: Lost braces; missing escapes or markup?
    14 | The {kdist} functions dk, pk, qk and rk, calculates the K-distribution
       |     ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ks’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
prepare_Rd: NEWS.Rd:58: Dropping empty section ‘kelvin INITIAL VERSION 1.0-0 (2012-05-30)’
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: ‘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.
Packages required but not available: 'equateIRT', 'mirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'tensorflow', 'tfruns'

Package suggested but not available for checking: ‘tfdatasets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'tensorflow', 'tfruns'

Package suggested but not available for checking: ‘tfdatasets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reticulate', 'tensorflow', 'plotly', 'echarts4r', 'magick'

Packages suggested but not available for checking: 'keras3', 'tfdatasets'

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: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'ks', 'cramer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                          ^
checkRd: (-1) kernelFactory.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{method}{Can be one of the following: POLynomial kernel function (\code{pol}), LINear kernel function (\code{lin}), Radial Basis kernel Function \code{rbf}), random choice (random={pol, lin, rbf}) (\code{random}), burn- in choice of best function (burn={pol, lin, rbf }) (\code{burn}). Use \code{random} or \code{burn} if you don't know in advance which kernel function is best.}
       |                                                                                                                                                                                                                                                                   ^
Packages required but not available: 'ks', 'plyr', 'GB2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘GA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) compute_all_tests.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_all_tests.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compute_all_tests.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_SCR_data.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shinyBS', 'shiny', 'DT', 'golem', 'plotly', 'rintrojs',
  'shinycssloaders', 'shinydashboard', 'shinydashboardPlus',
  'shinyhelper', 'shinyWidgets'

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggrepel', 'pgdraw', 'quanteda', 'RcppEigen'

Package suggested but not available for checking: ‘readtext’

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: 'tm', '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
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
Packages required but not available: 'caret', 'flextable'

Package suggested but not available for checking: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Note: skipping ‘KFAS.Rnw’ due to unavailable dependencies: 'lme4'
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) kfda.Rd:26: Lost braces
    26 |  \item{kpca.train}{An object of class "kpca". It has results of \code{kpca} function. (see{\code{\link[kernlab]{kpca}}} (in package \pkg{kernlab}))}
       |                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                          ^
checkRd: (-1) kfino_plot.Rd:52: Lost braces; missing escapes or markup?
    52 |        plus the OK values. Prediction corresponds to E[X_{t} | Y_{1...t}] 
       |                                                                  ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fdapace', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinythemes', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'pROC', 'plyr', 'reshape2', 'shiny', 'text2vec'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘shinyjs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggraph', 'tinysnapshot'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘elastic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggrepel', 'DT', 'gt'
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'pryr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'shinythemes', 'ggrepel', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'DNAmixturesLite', 'gRaven', 'gRbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'raster', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘psd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘knockoff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘questionr’

Package which this enhances but not available for checking: ‘ClustVarLV’

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 which this enhances but not available for checking: ‘rkward’
checkRd: (-1) klausuR.answ-class.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:18-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausuR.answ-class.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:107-109: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) klausur.Rd:114-116: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) klausur.Rd:121-123: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) klausur.Rd:147: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) klausur.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) klausur.Rd:152-155: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘coca’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gt', 'openxlsx', 'shiny', 'shinydashboard', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'GGally', 'ggforce', 'ggrepel', 'gstat', 'metR'

Packages suggested but not available for checking:
  'sf', 'spelling', 'RGeostats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'blink', 'plyr', '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'

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: ‘mlpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'factoextra', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'genieclust', 'Gmedian', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'phylogram', 'Rcpp'

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'openxlsx', 'RcppSimdJson'

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 required but not available: ‘pammtools’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'BiodiversityR', 'sf', 'ggpubr'

Package suggested but not available for checking: ‘kadmin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RefManageR’

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: 'plyr', 'reshape2'
Note: skipping ‘illusions.Rmd’ due to unavailable dependencies: 'plyr'
Note: skipping ‘maps.Rmd’ due to unavailable dependencies: 'reshape2'
Packages suggested but not available for checking: 'shiny', 'miniUI', 'DT'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'JuliaCall', 'magick', 'reticulate'
Package required but not available: ‘openxlsx’

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 suggested but not available for checking: ‘spelling’
Packages required but not available: 'parallelDist', 'forecast', 'plyr'

Package suggested but not available for checking: ‘tsibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'caret'

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: 'glmnet', 'RSpectra'

Packages suggested but not available for checking: 'ranger', 'RPtests'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bigmemory’

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:
  'raster', 'rgbif', 'usdm', 'car', 'candisc'
checkRd: (-1) MapPolygon.Rd:20: Lost braces
    20 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
checkRd: (-1) SurveyQ.Rd:26: Lost braces
    26 |   \item{shape}{If the estimators in the function link[KnowBR]{KnowBPolygon} were calculated using an external shape file, it is necessary to indicate the file in this argument. It is not necessary to select any polygon within the file, just to load the whole shape file.}
       |                                                              ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
Packages required but not available:
  'minerva', 'Rtsne', 'umap', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bigmemory’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'ggrepel', 'pbkrtest'

Packages suggested but not available for checking: 'devtools', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'tm', 'shiny', 'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcalg', 'energy', 'RSpectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) kpmt.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kpmt.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kpmt.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package required but not available: ‘anytime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) compose.Rd:13: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) compose.Rd:14: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
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: ‘anMC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spam’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rARPACK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) Predict_kernel_Ridge_MM.Rd:45: Lost braces; missing escapes or markup?
    45 |   and alpha_train is the BLUP of alpha for the model, i.e. alpha_train=Cov(alpha,Y_train)*Var(Y_train)^{-1}*(Y_train - E[Y_train]) }
       |                                                                                                        ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) ks_test_stat.Rd:14: Lost braces
    14 | are valid. See /code{LcKS} for accepted functions.}
       |                     ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pryr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
Package suggested but not available for checking: ‘FactoClass’
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: ‘dbscan’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ksharp.Rmd’ using rmarkdown

Quitting from lines 28-34 [unnamed-chunk-1] (ksharp.Rmd)
Error: processing vignette 'ksharp.Rmd' failed with diagnostics:
there is no package called 'dbscan'
--- failed re-building ‘ksharp.Rmd’

SUMMARY: processing the following file failed:
  ‘ksharp.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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘multicool’

Package suggested but not available for checking: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'imputeTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'GSE', 'Rcpp'

Package suggested but not available for checking: ‘tclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plyr', 'openxlsx'

Package suggested but not available for checking: ‘rockchalk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'survey', 'magick'
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'reshape2', 'RcppArmadillo'

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'aricode', 'caret', 'glmnet', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) predict.l2boost.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict.l2boost.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘osqp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rtsne’

Package suggested but not available for checking: ‘optpart’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'questionr', 'spelling'
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_labelled.Rmd’ using rmarkdown

Quitting from lines 537-541 [unnamed-chunk-44] (intro_labelled.Rmd)
Error: processing vignette 'intro_labelled.Rmd' failed with diagnostics:
there is no package called 'questionr'
--- failed re-building ‘intro_labelled.Rmd’

--- re-building ‘look_for.Rmd’ using rmarkdown

Quitting from lines 31-33 [unnamed-chunk-3] (look_for.Rmd)
Error: processing vignette 'look_for.Rmd' failed with diagnostics:
there is no package called 'questionr'
--- failed re-building ‘look_for.Rmd’

--- re-building ‘missing_values.Rmd’ using rmarkdown
--- finished re-building ‘missing_values.Rmd’

--- re-building ‘packed_columns.Rmd’ using rmarkdown
--- finished re-building ‘packed_columns.Rmd’

SUMMARY: processing the following files failed:
  ‘intro_labelled.Rmd’ ‘look_for.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'car', 'collapse'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘smooth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) ln_quantile_value.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ln_quantile_value.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'sf', 'spdep', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cld2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcmdr’
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Package required but not available: ‘ggtext’

Packages suggested but not available for checking:
  'miniUI', 'shiny', 'shinyjs', 'shinyWidgets', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RcppRoll’

Packages suggested but not available for checking:
  'cubature', 'sf', 'terra'

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: ‘lidR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'qs'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'interp', 'lhs', 'crs'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘spatialreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'reshape2', 'car'
Running examples in ‘Lahman-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ManagersHalf
> ### Title: ManagersHalf table
> ### Aliases: ManagersHalf
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library("dplyr")

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library("reshape2")
Error in library("reshape2") : there is no package called ‘reshape2’
Execution halted
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rLakeAnalyzer', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'sf', 'geosphere'

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: 'shiny', 'shinydashboard'

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: ‘PHSMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) lambda.r-package.Rd:71-74: Lost braces
    71 | x \%g\% y \%:=\% {
       |                  ^
Packages required but not available: 'car', 'narray', 'imputeTS', 'torch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘webmockr’
Packages required but not available: 'lamW', 'reshape2', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'fastGHQuad', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CDM', 'Rcpp', 'sirt', 'RcppArmadillo'

Package suggested but not available for checking: ‘TAM’

Package which this enhances but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'riskRegression', 'pec', 'prodlim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GenerateData.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GenerateData.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:59-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) landmix.estimator.Rd:67-74: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘emdbook’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
checkRd: (-1) DOS.Rd:34: Lost braces; missing escapes or markup?
    34 |         Band-specific sensor $G_{rescale}$ (gain). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
checkRd: (-1) DOS.Rd:37: Lost braces; missing escapes or markup?
    37 |         Band-specific sensor $B_{rescale}$ (bias). Require either gain and offset or Grescale and Brescale to convert DN to radiance.
       |                                 ^
Packages required but not available: 'Rcpp', 'terra', 'RcppArmadillo'

Packages suggested but not available for checking: 'raster', 'sf', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'fields', 'sf'

Packages suggested but not available for checking: 'shiny', 'shinyjs', '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.
Package suggested but not available for checking: ‘shiny’
Running examples in ‘langevitour-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: langevitour-shiny
> ### Title: Shiny bindings for langevitour
> ### Aliases: langevitour-shiny langevitourOutput renderLangevitour
> 
> ### ** Examples
> 
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'lme4', 'lmerTest'
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) LML.Rd:43: Lost braces
    43 |     is specified only with the \code{GD}, code{HME}, or \code{NSIS}
       |                                               ^
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
checkRd: (-1) MISS.Rd:106: Lost braces
   106 |   code{Fit$Imp}. In the presence of numerous missing values, say more
       |       ^
checkRd: (-1) Matrices.Rd:316: Lost braces
   316 |   Gauss-Hermite quadrature rules. A grid of order eqn{K} provides an
       |                                                      ^
checkRd: (-1) PMC.Rd:214: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |       ^
checkRd: (-1) PMC.Rd:214-215: Lost braces
   214 |   item{nu}{This is the degrees of freedom parameter \eqn{\nu}{nu} for
       |           ^
checkRd: (-1) caterpillar.plot.Rd:15: Lost braces
    15 |     code{demonoid.hpc}, \code{iterquad}, \code{laplace}, \code{pmc},
       |         ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'miniUI', 'shiny', 'shinydashboard', 'shinyWidgets'

Package suggested but not available for checking: ‘lares’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openxlsx', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘treemap’

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', 'caret', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fMultivar', 'heatmaply', 'plotly', 'geometry'

Package suggested but not available for checking: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EGAnet’

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.
Package suggested but not available for checking: ‘heplots’
GNU make is a SystemRequirements.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ade4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘quarto’
Packages suggested but not available for checking:
  'devtools', 'lme4', 'mixtools', 'fda', 'funFEM', 'dtwclust', 'mixAK',
  'mclustcomp', 'qqplotr', 'caret'
Running examples in ‘latrend-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lcMethodFlexmix
> ### Title: Method interface to flexmix()
> ### Aliases: lcMethodFlexmix
> 
> ### ** Examples
> 
> data(latrendData)
> if (require("flexmix")) {
+   method <- lcMethodFlexmix(Y ~ Time, id = "Id", time = "Time", nClusters = 3)
+   model <- latrend(method, latrendData)
+ }
Loading required package: flexmix
Loading required package: lattice
---------------------------------------------------------------------------
- Longitudinal clustering using: flexmix
---------------------------------------------------------------------------
Method arguments:
 formula.mb:     ~1
 time:           "Time"
 id:             "Id"
 nClusters:      3
 cluster:        NULL
 model:          NULL
 control:        NULL
 weights:        NULL
 formula:        Y ~ Time
---------------------------------------------------------------------------
Checking and transforming the training data format.
Preparing the training data for fitting...
Fitting the method...
Error in .checkPackageInstalled(name) : 
  The "lme4" package is required. Install the package to use this method.
	Run: install.packages("lme4")
Calls: latrend ... getREterms -> .loadOptionalPackage -> .checkPackageInstalled
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mpoly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘interp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spam', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘latticeExtra’
Packages suggested but not available for checking:
  'flextable', 'DiagrammeRsvg', 'tidySEM', 'spelling'
Packages required but not available: 'promises', 'shiny', 'DT', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DiagrammeRsvg’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinyAce', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'fastGHQuad', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Lavash', 'CVXR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'fields', 'lavaSearch2', 'lme4', 'mets', 'targeted'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'reshape2', 'RcppArmadillo'

Packages suggested but not available for checking:
  'lme4', 'lmerTest', 'pbkrtest', 'riskRegression'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'exdex', 'revdbayes'

Packages suggested but not available for checking:
  'extRemes', 'mev', 'texmex'

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', 'fstcore'

Packages suggested but not available for checking: 'fst', 'dipsaus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘forecast’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) univ.Rd:35: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:41: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:42: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:43: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:44: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:45: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) univ.Rd:46: Lost braces in \enumerate; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘RcppArmadillo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'shiny'

Package suggested but not available for checking: ‘shinyBS’

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: ‘shiny’

Packages suggested but not available for checking:
  'ggrepel', 'leaflet', 'leaflet.extras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
Packages required but not available:
  'DT', 'plotly', 'shiny', 'shinycssloaders', 'shinyjs', 'shinyWidgets'

Packages suggested but not available for checking: 'xcms', 'MSnbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘wdm’

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: ‘semPlot’

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyBS', 'shinydashboard', 'shinyWidgets', 'shinyalert',
  'shinybusy', 'shinyjs', 'shinycssloaders', 'DT', 'ldatuning',
  'topicmodels', 'textmineR', 'chinese.misc', 'ggrepel', 'qgraph',
  'factoextra', 'quanteda'

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: ‘tosca’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'reshape2', 'penalized'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'chinese.misc', 'DT', 'ldatuning', 'plotly', 'quanteda', 'shiny',
  'shinyalert', 'shinyBS', 'shinycssloaders', 'shinydashboard',
  'shinyjs', 'shinyWidgets', 'textmineR', 'tidytext', 'tm',
  'topicmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘folda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'extraDistr', 'topicmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'topicmodels', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'topicmodels', 'gistr', 'servr', 'shiny'
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'plyr', 'reshape2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'GUniFrac', 'castor', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'keras', 'devtools', 'reticulate', 'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'ashr', 'RcppArmadillo'

Package suggested but not available for checking: ‘updog’

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: ‘GA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'tdata'

Package suggested but not available for checking: ‘systemfit’

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: 'leaflet', 'shiny', 'shinyjs'

Packages suggested but not available for checking:
  'shinytest', 'raster', 'rmapshaper', 'shinycssloaders'

VignetteBuilder package required for checking but not installed: ‘shinycssloaders’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonsf', 'leaflet', 'raster', 'sf'

Packages suggested but not available for checking:
  'leafgl', 'lwgeom', 'mapdeck', 'plainview', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geojsonsf', 'jsonify', 'leaflet', 'sf'

Packages suggested but not available for checking: 'colourvalues', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'leaflet.extras'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

Packages suggested but not available for checking:
  'shiny', 'sf', 'geojsonsf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

Packages suggested but not available for checking:
  'shiny', 'manipulateWidget'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘V8’
Package required but not available: ‘raster’

Packages suggested but not available for checking:
  's2', 'sf', 'shiny', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geojsonsf', 'leaflet', 'leaflet.extras', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'sf'

Packages which this enhances but not available for checking:
  'geojsonio', 'mapedit', 'mapview', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lidR', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

Package suggested but not available for checking: ‘geojsonio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mvnfast’

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: ‘lhs’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) IPODFUN.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{H}{an N by N projection matrix X(X'X)^{-1}X' }
       |                                               ^
Package required but not available: ‘opencpu’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) S2mu.Rd:18: Lost braces; missing escapes or markup?
    18 | \code{S2mu} computes a estimation of the variance, given a sample {x} with known population mean (denoted by \code{mu}).
       |                                                                   ^
checkRd: (-1) sample.quantile.Rd:20: Lost braces; missing escapes or markup?
    20 | \code{sample.quantile} computes a estimation of different quantiles, given a sample {x}, using order statistics.
       |                                                                                     ^
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: ‘shiny’

Packages suggested but not available for checking:
  'ChemoSpec', 'ade4', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'promises', 'shiny'

Packages suggested but not available for checking:
  'httpuv', 'later', 'reticulate', 'shinytest2', 'sortable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘DiagrammeRsvg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'sf', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'glmmTMB', 'lme4', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'greybox', 'smooth', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pROC', 'glmnet', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Note: skipping ‘getting_started.Rmd’ due to unavailable dependencies:
  'devtools'
Packages required but not available: 'brms', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'sccore', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

Packages suggested but not available for checking:
  'bipartite', 'devtools', 'multinet', 'qpdf', '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: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘shiny’
Running examples in ‘leprechaun-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootstrap_version
> ### Title: Default Bootstrap Version
> ### Aliases: bootstrap_version
> 
> ### ** Examples
> 
> bootstrap_version()
Error in utils::packageVersion("shiny") : 
  there is no package called ‘shiny’
Calls: bootstrap_version -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'caret', 'wordspace'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'latticeExtra', 'openxlsx', '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: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'terra', 'geosphere', 'sf'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) hash_sentiment_slangsd.Rd:28-37: Lost braces
    28 | article{DBLP:journals/corr/Wu-etal16,
       |        ^
checkRd: (-1) hash_sentiment_slangsd.Rd:29: Lost braces; missing escapes or markup?
    29 |   author    = {Liang Wu and Fred Morstatter and Huan Liu},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:30-31: Lost braces
    30 |   title     = {SlangSD: Building and Using a Sentiment Dictionary of Slang 
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:32: Lost braces; missing escapes or markup?
    32 |   journal   = {CoRR},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:33: Lost braces; missing escapes or markup?
    33 |   volume    = {abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:34: Lost braces; missing escapes or markup?
    34 |   year      = {2016},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:35: Lost braces; missing escapes or markup?
    35 |   url       = {http://arxiv.org/abs/1608.05129},
       |               ^
checkRd: (-1) hash_sentiment_slangsd.Rd:36: Lost braces; missing escapes or markup?
    36 |   timestamp = {Wed, 17 Aug 2016 23:32:57 GMT}
       |               ^
checkRd: (-1) sw_python.Rd:32: Lost braces; missing escapes or markup?
    32 | * Neither the name of the {organization} nor the names of its
       |                           ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'quanteda', 'quanteda.textstats'

Packages suggested but not available for checking:
  'corpustools', 'tidytext', 'tm', 'pdftools', 'spelling', 'striprtf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyjs', 'shinythemes', 'shinyFiles', 'shinyMobile', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DESeq2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘lfc_vignette.Rmd’ using rmarkdown

Quitting from lines 35-47 [unnamed-chunk-1] (lfc_vignette.Rmd)
Error: processing vignette 'lfc_vignette.Rmd' failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘lfc_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘lfc_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'plyr', 'rARPACK'

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:
  'plm', 'cubature', 'alpaca'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'forecast', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSpectra', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'VIM', 'pcaMethods', 'reshape2', 'reshape', 'plotly'

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'latticeExtra', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'raster', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SKAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'bayesplot', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'np'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘elastic’
Package required but not available: ‘SKAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_for_LHD.Rmd’ using rmarkdown

Quitting from lines 26-28 [unnamed-chunk-2] (Vignette_for_LHD.Rmd)
Error: processing vignette 'Vignette_for_LHD.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘Vignette_for_LHD.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette_for_LHD.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) isingdata.Rd:14: Lost braces; missing escapes or markup?
    14 |     \item{X}{a 5000-by-100 matrix, each entry is in {-1,1}.}
       |                                                     ^
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'openxlsx', 'Rcpp'

Package suggested but not available for checking: ‘fmtr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'terra', 'sf', 'imager', 'car', 'reldist', 'lidR'

Packages suggested but not available for checking: 'stars', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rlas', 'sf', 'stars', 'terra', 'RcppArmadillo'

Packages suggested but not available for checking:
  'geometry', 'gstat', 'raster', 'RCSF', 'RMCC', 'mapview', 'mapedit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'markovchain', 'Rcpp'

Packages suggested but not available for checking:
  'demography', 'forecast', 'StMoMo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘LifeInsureR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openxlsx', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leaflet', 'shiny', 'leaflet.minicharts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maptiles', 'terra', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘openxlsx’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) lx_list_lights.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lx_list_lights.Rd:27: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Packages required but not available: 'flextable', 'ggtext', 'plotly'

Packages suggested but not available for checking:
  'gghighlight', 'gt', 'gtsummary'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pavo', 'spelling'
Packages required but not available: 'shiny', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘likelihoodAsy.Rnw’ using knitr

Quitting from lines 730-735 [Random intercept example] (likelihoodAsy.Rnw)
Error: processing vignette 'likelihoodAsy.Rnw' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘likelihoodAsy.Rnw’

SUMMARY: processing the following file failed:
  ‘likelihoodAsy.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) likelihood_calculation.Rd:24: Lost braces
    24 | For eqn{i = 1\dots N} independent observations in a vector \var{X}, with individual observations \eqn{x_i}{xi}, and a set of parameter values \eqn{\theta}:
       |        ^
checkRd: (-1) simulated_annealing_algorithm.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulated_annealing_algorithm.Rd:27: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'plyr'

Packages suggested but not available for checking: 'devtools', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'caret', 'glmnet', 'M3C', 'princurve', 'plyr', 'pROC',
  'reticulate', 'reshape', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'keras', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'text2vec', 'magick', 'keras', 'shiny', 'shinythemes', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'miniUI'

Package suggested but not available for checking: ‘Rtsne’

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: ‘ggrepel’
Running examples in ‘limonaid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: processLimeSurveyDropouts
> ### Title: Process LimeSurvey dropouts
> ### Aliases: processLimeSurveyDropouts
> 
> ### ** Examples
> 
> limonaid::processLimeSurveyDropouts(c(1,2,1,1,2,3,2,2,3,2,1));
Error in limonaid::processLimeSurveyDropouts(c(1, 2, 1, 1, 2, 3, 2, 2,  : 
  To process the LimeSurvey dropouts, you need to have both the {ggplot2} and {ggrepel} packages installed. You can install them with:

  install.packages(c('ggplot2', 'ggrepel'));
Execution halted
Packages required but not available: 'ashr', 'DESeq2', 'mashr'

Package suggested but not available for checking: ‘qs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 22-30 [unnamed-chunk-2] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'qs'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lamW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘terra’

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: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Running examples in ‘lineupjs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lineupOutput
> ### Title: Shiny bindings for lineup
> ### Aliases: lineupOutput renderLineup
> 
> ### ** Examples
> 
> # !formatR
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'leaflet.minicharts'

Packages suggested but not available for checking: 'sf', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'miniUI', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'sf', 'terra'

Package suggested but not available for checking: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'BGData', 'bigmemory'
Running examples in ‘LinkedMatrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ColumnLinkedMatrix-class
> ### Title: A Class for Linking Matrices by Columns or Rows
> ### Aliases: ColumnLinkedMatrix-class RowLinkedMatrix-class
> ### Keywords: classes
> 
> ### ** Examples
> 
> # Create various matrix-like objects that correspond in dimensions
> m1 <- ff::ff(initdata = rnorm(50), dim = c(5, 10))
> m2 <- bigmemory::big.matrix(init = rnorm(50), nrow = 5, ncol = 10)
Error in loadNamespace(x) : there is no package called ‘bigmemory’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'minerva', 'energy', 'shinybusy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘AER’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'tableone'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'ggiraph', 'rcompanion', 'ggrepel', 'reshape2', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DT’

Package which this enhances but not available for checking: ‘workflowr’
checkRd: (-1) ld_build_html_site.Rd:41: Lost braces
    41 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
checkRd: (-1) ld_create_doc.Rd:29: Lost braces
    29 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}}
       |                                                        ^
Running ‘testthat.r’ [12s/14s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  > library(listdown)
  > 
  > test_check("listdown")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 32 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-create-doc.r:27:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-make-chunks.r:2:1'): (code run outside of `test_that()`) ───────
  <packageNotFoundError/error/condition>
  Error in `library(DT)`: there is no package called 'DT'
  Backtrace:
      ▆
   1. └─base::library(DT) at test-make-chunks.r:2:1
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 32 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘listdown.rmd’ using rmarkdown

Quitting from lines 144-149 [unnamed-chunk-9] (listdown.rmd)
Error: processing vignette 'listdown.rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘listdown.rmd’

SUMMARY: processing the following file failed:
  ‘listdown.rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘miniUI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘litedown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pkg_desc
> ### Title: Print the package description, news, citation, manual pages, and
> ###   source code
> ### Aliases: pkg_desc pkg_news pkg_code pkg_citation pkg_manual
> 
> ### ** Examples
> 
> litedown::pkg_desc()
Error in detect_pkg() : 
  Cannot automatically detect the package root directory from '/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/litedown.Rcheck'. You must provide the package name explicitly.
Calls: <Anonymous> -> packageDescription -> detect_pkg
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'exdex', 'revdbayes', 'rust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'genio', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘stylo’
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) is_natural_number.Rd:17: Lost braces; missing escapes or markup?
    17 | Test for natural numbers according to ISO 80000-2, that is the set  {0, 1, 2, ...}
       |                                                                     ^
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) vcov.liu.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear Liu regression model for scalar or vector biasing parameter \code{d}{d} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{d}{d}.}
       |                                                                                                                             ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

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: ‘pROC’
Error(s) in re-building vignettes:
  ...
--- re-building ‘liver-example.Rmd’ using rmarkdown

Quitting from lines 21-26 [unnamed-chunk-2] (liver-example.Rmd)
Error: processing vignette 'liver-example.Rmd' failed with diagnostics:
there is no package called 'pROC'
--- failed re-building ‘liver-example.Rmd’

SUMMARY: processing the following file failed:
  ‘liver-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'glmnetUtils', 'lme4', 'pROC'

Package suggested but not available for checking: ‘caret’

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: 'StanHeaders', 'Rcpp', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'reghelper'

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: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'ggforce', 'fmdu', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'sommer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EMD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dynutils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'minqa', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'MEMSS', 'mlmRev', 'gamm4', 'pbkrtest', 'car', 'rr2', 'semEff',
  'merDeriv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mlmRev', 'lme4', 'merDeriv'
Packages required but not available: 'lme4', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggdist', 'HLMdiag'

Packages suggested but not available for checking: 'lme4', 'mlmRev'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘pbkrtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘lme4’
Running examples in ‘lmfor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plants
> ### Title: Sapling counts from sample plots of sapling stands in Finland.
> ### Aliases: plants
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(plants)
> library(lme4)
Error in library(lme4) : there is no package called ‘lme4’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘semPlot’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'bigmemory'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'sf', 'spam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggpubr', 'lme4', 'lmerTest', 'mice', 'Publish', 'reshape2'
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## * load packages
  > library(testthat)
  > library(LMMstar)
  LMMstar version 1.1.0
  
  Attaching package: 'LMMstar'
  
  The following object is masked from 'package:base':
  
      remove
  
  > 
  > library(data.table)
  > library(ggplot2)
  > library(lava)
  
  Attaching package: 'lava'
  
  The following object is masked from 'package:ggplot2':
  
      vars
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > library(lme4)
  Error in library(lme4) : there is no package called 'lme4'
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'SuperGauss', 'RcppEigen'

Package suggested but not available for checking: ‘mniw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Lmoments’

Package suggested but not available for checking: ‘copBasic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SPEI’
checkRd: (-1) lmomPi-Package.Rd:9: Lost braces
     9 | {\code{\link{cdf}}}{: generic distribution function;  }  
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:10: Lost braces
    10 | {\code{\link{qua}}}{: generic quantile function;  } 
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:11: Lost braces
    11 | {\code{\link{pel}}}{: fitting of probability distribution function through L-moments. }
       |                    ^
checkRd: (-1) lmomPi-Package.Rd:27: Lost braces; missing escapes or markup?
    27 | The function  \code{\link{spi.cdf}()} is compared against \code{SPEI::spi()} in SPEI package (\url{https://cran.r-project.org/package=SPEI}). The differences in SPI extimation have order of magnitude averagely about 10^{-8},  due to  the different fitting methods implemented in the two packages. 
       |                                                                                                                                                                                                                            ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
checkRd: (-1) vcov.Rd:20: Lost braces
    20 | A list of matrix of estimated covariances in the linear ridge regression model for scalar or vector biasing parameter \code{K}{K} is produced. Each list element has row and column names corresponding to the parameter names given by the \code{coef(mod)}. List items are named correspond to values of biasing parameter \eqn{K}{K}.}
       |                                                                                                                               ^
Skipping checking math rendering: package 'V8' unavailable
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'car', 'dynlm', 'AER'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'ranger', 'twang'
Packages required but not available: 'shiny', 'shinyjs', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'MatchIt', 'marginaleffects', 'PSweight', 'estimatr', 'ivreg'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'seqinr', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘tTestTable.rda’
Package suggested but not available for checking: ‘mcmcse’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppGSL'

Packages suggested but not available for checking:
  'plotly', 'bayesplot', 'censored', 'tidymodels', 'pec'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'caret', 'echarts4r', 'shinyAce', 'shinyjs', 'golem',
  'colourpicker', 'shinydashboard', 'shiny', 'shinycustomloader',
  'shinydashboardPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'OpenStreetMap', 'plyr'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'TMB', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sampleSelection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'oce', 'SynchWave'

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: ‘taxize’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘interp’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) Rvarlacf.Rd:104: Lost braces
   104 |         eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |            ^
checkRd: (-1) Rvarlacf.Rd:104: Lost braces; missing escapes or markup?
   104 |         eqn{(2s+1)^{-2}} (this was the default in versions prior to
       |                    ^
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) FootballBrain.Rd:15: Lost braces; missing escapes or markup?
    15 |     { } \tab {or \code{FBConcuss}=football player with concussion history} \cr
       |     ^
checkRd: (-1) HappyPlanetIndex.Rd:14: Lost braces; missing escapes or markup?
    14 |     { } \tab {\code{5}=South Asia, \code{6}=East Asia, \code{7}=former Communist countries}\cr
       |     ^
checkRd: (-1) RockandRoll2012.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) RockandRoll2015.Rd:17: Lost braces; missing escapes or markup?
    17 |     { } \tab {\code{Lifetime Achievement}, \code{Sideman}} \cr
       |     ^
checkRd: (-1) StudentSurvey.Rd:12: Lost braces; missing escapes or markup?
    12 |     \item{\code{Sex}}{code {F}=female or \code{M}=male}
       |                            ^
checkRd: (-1) SynchronizedMovement.Rd:16: Lost braces; missing escapes or markup?
    16 |     { } \tab {for High/Low Synchronization + High/Low Exertion}\cr
       |     ^
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘expectreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'RSpectra', 'bigsnpr', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggrepel', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metR’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package which this enhances but not available for checking: ‘logcondens’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘logcondens’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ks’

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:
  'botor', 'devtools', 'pander', 'shiny'
Running examples in ‘logger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: formatter_pander
> ### Title: Formats R objects with pander
> ### Aliases: formatter_pander
> 
> ### ** Examples
> 
> ## Don't show: 
> old <- logger:::namespaces_set()
> ## End(Don't show)
> log_formatter(formatter_pander)
> log_info("42")
Error: Please install the 'pander' package to use log_info
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro.Rmd’ using rmarkdown

Quitting from lines 73-77 [knitr-pander-setup] (Intro.Rmd)
Error: processing vignette 'Intro.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘Intro.Rmd’

--- re-building ‘anatomy.Rmd’ using rmarkdown
--- finished re-building ‘anatomy.Rmd’

--- re-building ‘customize_logger.Rmd’ using rmarkdown
--- finished re-building ‘customize_logger.Rmd’

--- re-building ‘migration.Rmd’ using rmarkdown
--- finished re-building ‘migration.Rmd’

--- re-building ‘performance.Rmd’ using rmarkdown
--- finished re-building ‘performance.Rmd’

--- re-building ‘r_packages.Rmd’ using rmarkdown
--- finished re-building ‘r_packages.Rmd’

--- re-building ‘write_custom_extensions.Rmd’ using rmarkdown
--- finished re-building ‘write_custom_extensions.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) analysis.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) analysis.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cookies', 'emayili', 'shiny', 'shinybusy', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rvinecopulib’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rARPACK’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fda', 'pROC', 'fda.usc'

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:
  'apollo', 'ggrepel', 'gtsummary', 'mixl'
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown
--- finished re-building ‘basic_usage.Rmd’

--- re-building ‘benchmark.Rmd’ using rmarkdown
--- finished re-building ‘benchmark.Rmd’

--- re-building ‘convergence.Rmd’ using rmarkdown
--- finished re-building ‘convergence.Rmd’

--- re-building ‘data_formatting.Rmd’ using rmarkdown
--- finished re-building ‘data_formatting.Rmd’

--- re-building ‘interactions.Rmd’ using rmarkdown
--- finished re-building ‘interactions.Rmd’

--- re-building ‘mnl_models.Rmd’ using rmarkdown
--- finished re-building ‘mnl_models.Rmd’

--- re-building ‘mnl_models_weighted.Rmd’ using rmarkdown
--- finished re-building ‘mnl_models_weighted.Rmd’

--- re-building ‘mxl_models.Rmd’ using rmarkdown
--- finished re-building ‘mxl_models.Rmd’

--- re-building ‘predict.Rmd’ using rmarkdown
--- finished re-building ‘predict.Rmd’

--- re-building ‘summarizing_results.Rmd’ using rmarkdown

Quitting from lines 108-112 [unnamed-chunk-11] (summarizing_results.Rmd)
Error: processing vignette 'summarizing_results.Rmd' failed with diagnostics:
there is no package called 'gtsummary'
--- failed re-building ‘summarizing_results.Rmd’

--- re-building ‘utility_models.Rmd’ using rmarkdown
--- finished re-building ‘utility_models.Rmd’

SUMMARY: processing the following file failed:
  ‘summarizing_results.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survey’
Running examples in ‘logmult-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: svygnm
> ### Title: Fitting Generalized Nonlinear Models With Complex Survey Data
> ### Aliases: svygnm svygnm.svyrep.design
> ### Keywords: models nonlinear
> 
> ### ** Examples
> 
>   library(survey)
Error in library(survey) : there is no package called ‘survey’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'shiny', 'plumber'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'miniUI', 'shiny', 'waiter'

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', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'reshape2', 'transport', 'dbscan', 'alphashape3d'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survminer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'reshape2', 'glmmTMB', 'bestNormalize', 'car', 'rstatix'

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: ‘AICcmodavg’

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: ‘fdapace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘StatMatch’

Packages suggested but not available for checking:
  'FactoMineR', 'factoextra', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'ggpubr', 'plyr', 'QSutils', 'reshape2', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'fdapace', 'grf', 'lme4', 'mvnfast', 'plyr', 'refund', 'fda',
  'fda.usc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TDAstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SAheart.Rd:96: Lost braces
    96 |   J.E. Rossouw, J.P.D. Plessis, A.J.S. Benad\'{e}, P.C.J. Jordaan, 
       |                                               ^
checkRd: (-1) SAheart.Rd:97: Lost braces
    97 |   J.P. Kotz\'{e}, P.L. Jooste, and J.J. Ferreira (1983)
       |              ^
Package suggested but not available for checking: ‘GGally’
Package suggested but not available for checking: ‘rworldmap’
checkRd: (-1) l_binCut.Rd:30: Lost braces
    30 | when 'code{labels = FALSE}, the default \code{active} is  \code{-1}; and when \code{labels} is a vector of length equal
       |           ^
Packages required but not available: 'shiny', 'colourpicker'

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:
  'bayesplot', 'brms', 'rstan', 'rstanarm', 'rstantools', 'spdep'
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: ‘rstan’
Error(s) in re-building vignettes:
  ...
--- re-building ‘LoRaD-gtrig-vignette.Rmd’ using rmarkdown
--- finished re-building ‘LoRaD-gtrig-vignette.Rmd’

--- re-building ‘bridge-sampling.Rmd’ using rmarkdown

Quitting from lines 34-37 [unnamed-chunk-2] (bridge-sampling.Rmd)
Error: processing vignette 'bridge-sampling.Rmd' failed with diagnostics:
there is no package called 'rstan'
--- failed re-building ‘bridge-sampling.Rmd’

--- re-building ‘lorad-k80-vignette.Rmd’ using rmarkdown
--- finished re-building ‘lorad-k80-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘bridge-sampling.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'GA', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rARPACK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'ggpubr', 'DescTools', 'HH'

Packages suggested but not available for checking: 'ggrepel', 'DESeq2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcaMethods', 'geomorph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package 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'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘multimode’
Running examples in ‘LPCM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ms.rep
> ### Title: Mean shift procedures.
> ### Aliases: ms.rep meanshift ms.rep.min
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(stamps, package="multimode")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘multimode’
Calls: data -> find.package
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'virtualspecies', 'terra'

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: 'plm', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'apcluster', 'LPGraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'glmnet', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘LPGraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘MomTrunc’

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: ‘reshape’
Running examples in ‘lrd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crp_multiple
> ### Title: Conditional Response Probability for Multiple Lists
> ### Aliases: crp_multiple
> ### Keywords: correct free position proportion recall scoring serial
> 
> ### ** Examples
> 
> 
> data("multi_data")
> data("multi_answers")
> 
> DF_long <- arrange_data(data = multi_data,
+                        responses = "Response",
+                        sep = " ",
+                        id = "Sub.ID",
+                        repeated = "List.Number")
> 
> library(reshape)
Error in library(reshape) : there is no package called ‘reshape’
Execution halted
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'shiny'

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'BIFIEsurvey', 'TAM', 'miceadds', 'sirt', 'mice', 'difR', 'kerdiest',
  'glmnet', 'mirt', 'car', 'mitml', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tm’
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plyr', 'reshape2', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TSdist’

Package suggested but not available for checking: ‘LSDsensitivity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'LSDinterface', 'LSDsensitivity'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'LSDinterface', 'sensitivity', '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
Packages required but not available:
  'Rcpp', 'pROC', 'plotly', 'plyr', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘seqinr’

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:
  'raster', 'rasterVis', 'latticeExtra'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'quanteda', 'quanteda.textstats', 'RSpectra', 'rsparse', 'proxyC',
  'ggrepel', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'rTensor2', 'gsignal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GDINA', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'metajam', 'sf', 'ggmap', 'leaflet', 'tsibble', 'feasts', 'gt'
Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tmle', 'arm'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) k.Rd:27: Lost braces
    27 |  code{\link{ACSPlan-class}}, 
       |      ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ipred', 'prodlim'

Package suggested but not available for checking: ‘LTRCtrees’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘icenReg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcpp’
GNU make is a SystemRequirements.
Packages required but not available: 'rpostgis', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'sommer'
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lucid)
  > 
  > test_check("lucid")
    id P1 P2          P3
  1  A  a -1 3.3175e-140
  2  B  b  0 1.0637e-165
  3  C c   1 1.1279e-157
    id P1 P2
  1  A  a -1
  2  B  b  0
  3  C c   1
                                                                                                                                                  P3
  1 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000332
  2 0                                                                                                                                               
  3 0                                                                                                                                               
        effect variance stddev
   (Intercept)   615.3  24.81 
      Residual    16.17  4.021
  [ FAIL 3 | WARN 4 | SKIP 2 | PASS 19 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • empty test (2): 'test_lucid.R:150:1', 'test_vc.R:74:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_vc.R:36:3'): lmer ──────────────────────────────────────────────
  Error in `lmer(travel ~ 1 + (1 | Rail), data = Rail)`: could not find function "lmer"
  ── Error ('test_vc.R:56:3'): glmer ─────────────────────────────────────────────
  Error in `glmer(travel ~ 1 + (1 | Rail), data = Rail, family = gaussian(link = "log"))`: could not find function "glmer"
  ── Error ('test_vc.R:97:3'): mmer ──────────────────────────────────────────────
  Error in `mmer(travel ~ 1, random = ~Rail, data = Rail)`: could not find function "mmer"
  
  [ FAIL 3 | WARN 4 | SKIP 2 | PASS 19 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lucid_examples.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/lucid.Rcheck/vign_test/lucid/vignettes/lucid_examples_files/figure-html/dotplot-1.png
576x384 pixels, 8 bits/pixel, 256 colors in palette
Input IDAT size = 12906 bytes
Input file size = 13776 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11859
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 11621
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 11621

Output IDAT size = 11621 bytes (1285 bytes decrease)
Output file size = 12479 bytes (1297 bytes = 9.41% decrease)


Quitting from lines 213-216 [lme4] (lucid_examples.Rmd)
Error: processing vignette 'lucid_examples.Rmd' failed with diagnostics:
could not find function "lmer"
--- failed re-building ‘lucid_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘lucid_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
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: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rasterVis'

Packages suggested but not available for checking: 'caret', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'interp', 'lamW', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'spelling', 'plotly', 'pander', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

Packages suggested but not available for checking:
  'torchvision', 'tfevents'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'lme4', 'lmerTest'
Error(s) in re-building vignettes:
  ...
--- re-building ‘accuracy_indices.Rmd’ using rmarkdown
--- finished re-building ‘accuracy_indices.Rmd’

--- re-building ‘working_with_models.Rmd’ using rmarkdown

Quitting from lines 28-30 [setup] (working_with_models.Rmd)
Error: processing vignette 'working_with_models.Rmd' failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘working_with_models.Rmd’

SUMMARY: processing the following file failed:
  ‘working_with_models.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'OpenMx', 'qgraph', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘depth’
checkRd: (-1) geom_lv.Rd:101: Lost braces; missing escapes or markup?
   101 | determines whether the width of the box for letter value LV(i) should be proportional to i (linear), proportional to $2^{-i}$ (height), or  whether
       |                                                                                                                         ^
checkRd: (-1) geom_lv.Rd:102: Lost braces; missing escapes or markup?
   102 | the area of the box should be proportional to $2^{-i}$ (area).}
       |                                                  ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'units', 'sf'

Package suggested but not available for checking: ‘geosphere’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'gWQS', 'gamm4'

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: 'geosphere', 'caret'

Packages suggested but not available for checking:
  'adehabitatLT', 'moveHMM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mpoly', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘InterSIM’

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: ‘TestDesign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘icenReg’

Packages suggested but not available for checking:
  'mixtools', 'Epi', 'ks', 'multimode'

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: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recipes’

Packages suggested but not available for checking:
  'adabag', 'BART', 'C50', 'censored', 'glmnet',
  'ParBayesianOptimization', 'ranger', 'rBayesianOptimization'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phenocamr', 'sf'

Packages suggested but not available for checking: 'leaflet', 'clifro'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'raster', 'sf', 'terra'

Package suggested but not available for checking: ‘rnaturalearthhires’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mediation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'textmineR', 'tidytext', 'udpipe', 'shiny', 'shinythemes', 'tm',
  'hwordcloud', 'topicmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'textmineR', 'tidytext', 'udpipe', 'shiny', 'shinythemes', 'tm',
  'hwordcloud', 'topicmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mada-data.Rd:45: Lost braces
    45 | Kriston, L., H{\"o}elzel, L., Weiser, A., Berner, M., & Haerter, M. (2008).\dQuote{ Meta-analysis: Are 3
       |               ^
Skipping checking math rendering: package 'V8' unavailable
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:
  'rstan', 'Rcpp', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘terra’
checkRd: (-1) toolAggregate.Rd:49: Lost braces; missing escapes or markup?
    49 | If {rel} is missing \code{to} refers to the aggregation target dimension name.}
       |    ^
checkRd: (-1) toolGetMapping.Rd:18: Lost braces
    18 | and rda (which needs to have the data stored with the object name "data"!). Use code{\link{toolConvertMapping}}
       |                                                                                     ^
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tidytext', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lpjmlkit', 'quitte', 'raster', 'terra'
Packages required but not available: 'Rcpp', 'GMMAT', 'RcppArmadillo'

Package suggested but not available for checking: ‘SeqVarTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'imager', 'fst'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘magick’

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', 'pdftools', 'tesseract'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'roptim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'Rcpp'

Packages suggested but not available for checking:
  'gganimate', 'plotly', 'transformr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Packages suggested but not available for checking:
  'dittoSeq', 'vcr', 'webmockr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'lme4', 'plyr', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'miniUI'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DT', 'golem', 'openxlsx', 'sf', 'shiny', 'tmap', 'tmaptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'GGally', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'shiny', 'shinyjs', 'shinyBS'

Packages suggested but not available for checking: 'rstan', 'INLA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nomnoml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) makeProject.Rd:34: Lost braces
    34 | email{noahsilverman@ucla.edu}
       |      ^
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'terra', 'tidyterra', 'ows4R'

Package suggested but not available for checking: ‘rdhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) create_terminal_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
checkRd: (-1) full_repo_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                              ^
checkRd: (-1) full_repo_dir.Rd:11: Lost braces; missing escapes or markup?
    11 | the following child folders: {repo_base}/bin/ and {repo_base}/src/. A
       |                                                   ^
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'oro.nifti', 'oro.dicom', 'imager', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) manet.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) manet.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mixtbern.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MangroveTree.Rd:37: Lost braces
    37 |       An object of class \\code{\link[Mangrove]{MangrovePed}}
       |                                ^
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'DT'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘RcppArmadillo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'miniUI', 'shinyjs'

Packages suggested but not available for checking: 'leaflet', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DescTools’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘GFD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'keras', 'ggcorrplot', 'reshape2', 'scutr'

Package suggested but not available for checking: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘manynet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'semPlot', 'semptools', 'Amelia', 'mice'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggraph’

Packages suggested but not available for checking:
  'concaveman', 'gganimate', 'ggforce', 'graphlayouts', 'learnr',
  'netdiffuseR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reticulate', 'lhs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RSpectra', 'Rtsne', 'labdsv', 'dbscan', 'RcppArmadillo',
  'RcppDist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'smooth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mrgsolve’

Package suggested but not available for checking: ‘minqa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'slippymath', 'protolite', 'geojsonsf', 'magick', 'leaflet',
  'units', 'raster'

Packages suggested but not available for checking:
  'ggspatial', 'mapdeck', 'tigris', 'tidycensus', 'tmap', 'mapboxer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geojsonsf’

Package suggested but not available for checking: ‘shiny’

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:
  'colourvalues', 'googlePolylines', 'geojsonsf', 'jsonify', 'Rcpp',
  'shiny', 'sfheaders', 'geometries', 'interleave', 'spatialwidget'

Packages suggested but not available for checking:
  'googleway', 'spatialwidget'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leafem', 'leaflet', 'leaflet.extras', 'leafpm', 'mapview', 'miniUI',
  'raster', 'sf', 'shiny'

Package which this enhances but not available for checking: ‘geojsonio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'deformula', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonsf', 'sf', 'terra'

Packages suggested but not available for checking: 'shiny', 'mapboxapi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

Package suggested but not available for checking: ‘geosphere’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'Rcpp'

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Packages suggested but not available for checking: 'mapsf', 'terra'

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: 'sf', 'terra'

Packages suggested but not available for checking:
  'exactextractr', 'landscapemetrics', 'rstac'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'geosphere'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'colourpicker', 'ggspatial', 'sf', 'shiny', 'shinyFeedback',
  'shinyjs', 'shinyWidgets', 'waiter'

Packages suggested but not available for checking: 'shinytest2', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'tmap', 'cartography', 'sf', 'leaflet', 'tmaptools', 'leafpop',
  'leafsync', 'mapview', 'geojsonio', 's2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'fields', 'ggpubr', 'reshape2', 'smacof', 'princurve',
  'vcfR', 'plotly'

Packages suggested but not available for checking: 'updog', 'polymapR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sf', 'stars'

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'magick', 'pdftools', 'raster', 'Rcpp', 'RNiftyReg', 'sf',
  'slippymath'

Packages suggested but not available for checking:
  'lwgeom', 'mapview', 'mmand', 'osmdata', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sf’
Running examples in ‘mapsFinland-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mkMapFinland
> ### Title: Make map of Finland
> ### Aliases: mkMapFinland
> 
> ### ** Examples
> 
> hv.alueet<-mkMapFinland(url="https://tinyurl.com/hvalueet2022")
trying URL 'https://tinyurl.com/hvalueet2022'
downloaded 1.1 MB

Error in loadNamespace(x) : there is no package called ‘sf’
Calls: mkMapFinland ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 's2', 'sf'

Packages suggested but not available for checking:
  'terra', 'Ckmeans.1d.dp', 'lwgeom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'giscoR', 'sf'

Packages suggested but not available for checking:
  'leaflet', 'slippymath', 'terra', 'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rnaturalearth’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'terra', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'sf', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'terra', 'slippymath'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'leafem', 'leaflet', 'leafpop', 'raster', 'satellite', 'servr', 'sf'

Packages suggested but not available for checking:
  'later', 'leaflet.extras2', 'leafsync', 'lwgeom', 'mapdeck',
  'plainview', 's2', 'stars', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘grf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘seacarb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'devtools', 'scholar', 'tidytext', 'treemapify', 'widyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'AER', 'Amelia', 'afex', 'bife', 'blme', 'brms', 'brmsmargins',
  'car', 'clarify', 'cjoint', 'collapse', 'crch', 'estimatr', 'fixest',
  'flexsurv', 'ggdist', 'ggrepel', 'glmmTMB', 'glmtoolbox', 'ivreg',
  'lme4', 'lmerTest', 'logistf', 'MatchIt', 'MCMCglmm', 'missRanger',
  'mice', 'miceadds', 'mlr3verse', 'optmatch', 'ordbetareg', 'phylolm',
  'plm', 'Rchoice', 'REndo', 'reticulate', 'robustlmm', 'rstanarm',
  'rstantools', 'rstpm2', 'sampleSelection', 'spelling', 'survey',
  'tidymodels', 'tinysnapshot', 'altdoc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘lme4’

Packages which this enhances but not available for checking:
  'AER', 'survey'
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) marima.Rd:28: Lost braces; missing escapes or markup?
    28 | ( if(is.ts(DATA)) { DATA <- as.matrix(data.frame(DATA)) } and a message
       |                   ^
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
Packages required but not available: 'shiny', 'shinyAce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'Rcpp', 'TMB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RSpectra', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ape', 'phangorn', 'geiger', '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: ‘ctmcd’

Package which this enhances but not available for checking: ‘etm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metR’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'bib2df', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'gdistance', 'geosphere', 'raster', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘parsec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
checkRd: (-1) marqLevAlg-package.Rd:14: Lost braces; missing escapes or markup?
    14 | (GH^{-1}G).
       |     ^
Package suggested but not available for checking: ‘gt’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(marquee)
  > 
  > test_check("marquee")
  [ FAIL 1 | WARN 0 | SKIP 9 | PASS 68 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • On CRAN (7): 'test-glue.R:8:3', 'test-grob.R:16:3', 'test-style.R:5:3',
    'test-style_helpers.R:29:3', 'test-style_set.R:2:3', 'test-style_set.R:31:3',
    'test-style_set.R:51:3'
  • On Linux (2): 'test-grob.R:51:3', 'test-parse.R:11:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-images.R:12:3'): images are picked up ──────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'gt'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-images.R:12:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 9 | PASS 68 ]
  Deleting unused snapshots:
  • grob/marquee_grob.png
  • parse/parsed.csv
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘marquee.Rmd’ using rmarkdown

Quitting from lines 11-22 [unnamed-chunk-1] (marquee.Rmd)
Error: processing vignette 'marquee.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘marquee.Rmd’

--- re-building ‘marquee_style.Rmd’ using rmarkdown
--- finished re-building ‘marquee_style.Rmd’

--- re-building ‘marquee_syntax.Rmd’ using rmarkdown
--- finished re-building ‘marquee_syntax.Rmd’

SUMMARY: processing the following file failed:
  ‘marquee.Rmd’

Error: Vignette re-building failed.
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: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'forecast', 'marssTMB'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Learning_MARSS.Rmd’ using rmarkdown
--- finished re-building ‘Learning_MARSS.Rmd’

--- re-building ‘Quick_Start.Rmd’ using rmarkdown

Quitting from lines 266-268 [unnamed-chunk-9] (Quick_Start.Rmd)
Error: processing vignette 'Quick_Start.Rmd' failed with diagnostics:
there is no package called 'forecast'
--- failed re-building ‘Quick_Start.Rmd’

--- re-building ‘EMDerivation.Rnw’ using Sweave
--- finished re-building ‘EMDerivation.Rnw’

--- re-building ‘Residuals.Rnw’ using Sweave
--- finished re-building ‘Residuals.Rnw’

--- re-building ‘UserGuide.Rnw’ using Sweave
--- finished re-building ‘UserGuide.Rnw’

SUMMARY: processing the following file failed:
  ‘Quick_Start.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

Packages suggested but not available for checking:
  'clusterProfiler', 'factoextra', 'FactoMineR', 'ggrepel', 'MAST',
  'reshape2'

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:
  'devtools', 'forestinventory', 'sae'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'survey', 'rpms', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ashr', 'plyr', 'Rcpp', 'RcppArmadillo', 'RcppGSL'

Packages suggested but not available for checking: 'flashier', 'ebnm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

Packages suggested but not available for checking: 'dismo', 'wallace'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) hr_levels.Rd:9-12: Lost braces
     9 | kernelBiweight <- function(x, mean = 0, sd = 1) {
       |                                                 ^
checkRd: (-1) hr_levels.Rd:33-36: Lost braces
    33 | kernelCosine <- function(x, mean = 0, sd = 1) {
       |                                               ^
checkRd: (-1) hr_levels.Rd:41-44: Lost braces
    41 | kernelEpanechnikov <- function(x, mean = 0, sd = 1) {
       |                                                     ^
checkRd: (-1) hr_levels.Rd:58-61: Lost braces
    58 | kernelOptCosine <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:65-68: Lost braces
    65 | kernelRectangular <- function(x, mean = 0, sd = 1) {
       |                                                    ^
checkRd: (-1) hr_levels.Rd:72-75: Lost braces
    72 | kernelSquaredCosine <- function(x, mean = 0, sd = 1) {
       |                                                      ^
checkRd: (-1) hr_levels.Rd:79-82: Lost braces
    79 | kernelTriangular <- function(x, mean = 0, sd = 1) {
       |                                                   ^
checkRd: (-1) hr_levels.Rd:86-89: Lost braces
    86 | kernelTricube <- function(x, mean = 0, sd = 1) {
       |                                                ^
checkRd: (-1) hr_levels.Rd:93-96: Lost braces
    93 | kernelTriweight <- function(x, mean = 0, sd = 1) {
       |                                                  ^
checkRd: (-1) hr_levels.Rd:100-103: Lost braces
   100 | kernelUniform <- function(x, mean = 0, sd = 1) {
       |                                                ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) CF2004.Rd:8: Lost braces; missing escapes or markup?
     8 |   \item{X2}{an optional second variable with same length as \code{X}, should the equation be multiple (see Details) {in mm}}
       |                                                                                                                     ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'flextable', 'ggrepel', 'ggspatial', 'maptiles', 'sf', 'tidyterra',
  'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'repmis', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
checkRd: (-1) Rand.index.Rd:22: Lost braces; missing escapes or markup?
    22 | The two vectors \code{x} and \code{y} must have equal length. Given a set \eqn{S} and two partitions \eqn{X} and \eqn{Y} of \eqn{S}, the Rand index is the proportion of pairs of elements in \eqn{S} (out of all pairs) that are either concordant in both \eqn{X} and \eqn{Y} (i.e., they belong to the same member of \eqn{X} and to the same member of \eqn{Y}) or discordant (i.e., not concordant) in both \eqn{X} and {Y}.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                              ^
checkRd: (-1) predict.matchFeat.Rd:21: Lost braces
    21 | The function \code{predict.matchFeat} finds the best matching for new feature vectors relative to an existing set of cluster/class centers. If code{object} results from a call to \code{\link{match.gaussmix}}, the same function is used for prediction (with fixed mean vectors and covariance matrices). In other cases, the function \code{\link{match.template}} is used for prediction. 
       |                                                                                                                                                    ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'optmatch', 'CBPS', 'glmnet', 'marginaleffects', 'highs', 'gurobi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rcbsubset', 'plyr', 'weights'

Packages suggested but not available for checking: 'optmatch', 'rrelaxiv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Match.Rd:90: Lost braces; missing escapes or markup?
    90 | expression in braces. For example, the condition "{[ab]*}" is equivalent
       |                                                   ^
Packages required but not available: 'MatchIt', 'mice', 'survey'

Package suggested but not available for checking: ‘Amelia’

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: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘js’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘rolog’

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.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

Package suggested but not available for checking: ‘webshot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'plotly', 'DT', 'shinydashboard', 'shinyWidgets', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bigmemory’
Package required but not available: ‘caret’

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', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

Packages suggested but not available for checking: 'devtools', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RSpectra', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'reshape2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Matrix_eQTL_main.Rd:31: Lost braces; missing escapes or markup?
    31 |     {genepos} in the call of \code{Matrix_eQTL_main} function.
       |     ^
checkRd: (-1) Matrix_eQTL_main.Rd:35: Lost braces; missing escapes or markup?
    35 |     the data frames \code{snpspos} and {genepos}.
       |                                        ^
Package 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', 'plyr', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
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.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘reshape2’
Packages suggested but not available for checking:
  'PMCMRplus', 'car', 'cosinor', 'cosinor2'
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘utilities.R’
Package required but not available: ‘beastier’

Packages suggested but not available for checking: 'beautier', 'tracerer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CVXR', 'glmnet', 'SIHR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lhs’
Running examples in ‘maximin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maximin
> ### Title: Space-filling design under the criterion of maximin distance
> ### Aliases: maximin maximin.cand
> ### Keywords: space-filling design computer experiment maximin distance
> 
> ### ** Examples
> 
>    
>  ## Not run: 
> ##D    ## maximin.cand
> ##D    # generate the design
> ##D    library("lhs")
> ##D    n <- 100
> ##D    p <- 2
> ##D    Xorig <- randomLHS(10, p)
> ##D    x1 <- seq(0, 1, length.out=n)
> ##D    Xcand <- expand.grid(replicate(p, x1, simplify=FALSE))
> ##D    names(Xcand) <- paste0("x", 1:2)
> ##D    T <- nrow(Xcand)
> ##D    Xsparse <- maximin.cand(n=n, Xcand=Xcand, Tmax=T, Xorig=Xorig, 
> ##D                            init=NULL, verb=FALSE, tempfile=NULL)
> ##D    
> ##D    maxmd <- as.numeric(format(round(max(na.omit(Xsparse$mis)), 5), nsmall=5))
> ##D    
> ##D    # visualization
> ##D    par(mfrow=c(1, 2))
> ##D    X <- Xcand[Xsparse$inds,]
> ##D    plot(X$x1, X$x2, xlab=expression(x[1]), ylab=expression(x[2]), 
> ##D         xlim=c(0, 1), ylim=c(0, 1), 
> ##D         main=paste0("n=", n, "_p=", p, "_maximin=", maxmd))
> ##D    points(Xorig, col=2, pch=20)
> ##D    abline(h=c(0, 1), v=c(0, 1), lty=2, col=2)
> ##D    if(!is.null(Xorig))
> ##D    {
> ##D      legend("topright", "Xorig", xpd=TRUE, horiz=TRUE, 
> ##D             inset=c(-0.03, -0.05), pch=20, col=2, bty="n")
> ##D    }
> ##D    plot(log(na.omit(Xsparse$mis)), type="b", 
> ##D         xlab="iteration", ylab="log(minimum distance)", 
> ##D         main="progress on minimum distance")
> ##D    abline(v=n, lty=2)
> ##D    mtext(paste0("design size=", n), at=n, cex=0.6)
> ##D    
> ##D   
> ## End(Not run)
>   
>   ## maximin
>   # generate the design
>   library("lhs")
Error in library("lhs") : there is no package called ‘lhs’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘raster’

Package suggested but not available for checking: ‘dismo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mev’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leaflet', 'MazamaCoreUtils', 'MazamaSpatialUtils'

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:
  'MazamaSpatialUtils', 'MazamaCoreUtils', 'sf', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'MazamaCoreUtils', 'rmapshaper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MazamaCoreUtils', 'MazamaRollUtils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
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: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rmixmod’

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'OpenMx', 'sem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bigmemory', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'terra'

Packages suggested but not available for checking: 'spsurvey', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘chipPCR’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'keras', 'Rtsne', 'pROC', 'reshape2', 'reticulate',
  'tensorflow'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘reshape2’

Packages suggested but not available for checking: 'ggdist', 'netmeta'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘ggdist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'fields', 'BayesX', 'kangar00'
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) SIGMAS.Rd:17: Lost braces; missing escapes or markup?
    17 | Sigmahat =  (Y^{T} Y)/n;
       |                ^
checkRd: (-1) SIGMAS.Rd:18: Lost braces; missing escapes or markup?
    18 | Sigmahat_fit = (Y^{T}  P_fx  Y)/n;
       |                   ^
checkRd: (-1) matpower.Rd:17: Lost braces; missing escapes or markup?
    17 | The function computes M^{power} for a symmetric matrix M. }
       |                         ^
Skipping checking math rendering: package 'V8' unavailable
Found the following HTML validation problems:
compile_sbtests.html:31:1 (compile_sbtests.Rd:29): Warning: trimming empty <li>
dorepart.html:93:1 (dorepart.Rd:47): Warning: trimming empty <li>
dosequa.html:94:1 (dosequa.Rd:49): Warning: trimming empty <li>
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Epi', 'Rcpp', 'highs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggrepel', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'babette', 'beautier', 'beastier', 'devtools', 'mauricer'

Packages suggested but not available for checking:
  'ape', 'hunspell', 'nLTT', 'phangorn', 'spelling', 'tracerer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking: 'PracTools', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pROC', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'wordcloud', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'faraway'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GA', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) MCbound.precalc1.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCbound.precalc1.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
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', 'tm'

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', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘geometry’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘plyr’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mcmcderive)
  > 
  > test_check("mcmcderive")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 31 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-mcmc-derive.R:197:3'): mcmc_derive in parallel ─────────────────
  Error in `eval(code, test_env)`: Plyr is required to run mcmc_derive on chains in parallel.
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-mcmc-derive.R:197:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─mcmcderive::mcmc_derive(...)
   5. └─mcmcderive:::mcmc_derive.mcmcr(...)
   6.   └─mcmcderive:::split_apply_combine(...)
   7.     └─chk::err("plyr is required to run mcmc_derive on chains in parallel")
   8.       └─rlang::abort(msg, class = class, !!!args[named], call = call)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 31 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘bayesplot’
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagnostic-pkgs.Rmd’ using rmarkdown

Quitting from lines 85-86 [unnamed-chunk-8] (diagnostic-pkgs.Rmd)
Error: processing vignette 'diagnostic-pkgs.Rmd' failed with diagnostics:
there is no package called 'bayesplot'
--- failed re-building ‘diagnostic-pkgs.Rmd’

--- re-building ‘faq.Rmd’ using rmarkdown
Loading required package: coda
--- finished re-building ‘faq.Rmd’

SUMMARY: processing the following file failed:
  ‘diagnostic-pkgs.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ape', 'cubature'

Package suggested but not available for checking: ‘bayesm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MCMCglmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MCMCglmm’

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', 'RcppEigen'

Packages suggested but not available for checking:
  'spdep', 'sf', 'bayesplot', 'survey'

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: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘cmdstanr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ecr', 'grapherator', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidybayes', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magick', 'odbc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'shinydashboard', 'flextable', 'Rcpp', 'RcppNumerical',
  'RcppEigen'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'bayesplot', 'tidybayes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘SMR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DescTools', 'mcr', 'pROC', 'VCA'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'robslopes', 'mixtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘robslopes’

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
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'trend', 'reshape2', 'lmomco'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
Packages required but not available: 'reshape2', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘diffmatchpatch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'logistf', 'Rcpp', 'pcalg', 'mgm', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ranger', 'Rcpp', 'splines2', '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: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'psqn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) normalizeWithMA.Rd:19: Lost braces
    19 |         \item{expGroup}{ a \code{vector} of experimental grouping variable such as plate. The length of code{expGroup} must be same as the number of rows of \code{mD}.}
       |                                                                                                             ^
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shinydashboard', 'DT', 'leaflet', 'leaflet.extras', 'shinyjs',
  'plotly', 'shinyWidgets', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CDM', 'miceadds', 'Rcpp', 'sirt', 'RcppArmadillo'

Packages which this enhances but not available for checking:
  'JointAI', 'jomo', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) mdp_example_forest.Rd:36: Lost braces; missing escapes or markup?
    36 | Let {1, ... S} be the states of the forest. the Sth state being the oldest.
       |     ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'smacof', 'princurve', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'smacof', 'clusterSim', 'symbolicDA', 'animation', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘webshot2’

Packages suggested but not available for checking:
  'leaflet', 'macleish', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dcm2', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking: 'cmdstanr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dynlm', 'hdrcde'

Packages suggested but not available for checking: 'car', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'fda', 'glme'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'microeco', 'reshape2', 'ggpubr'

Packages suggested but not available for checking:
  'rgexf', 'ape', 'file2meco'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'microeco', 'GUniFrac', 'ggpubr', 'lmerTest', 'glmmTMB'

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) bhm.mcmc.Rd:37: Lost braces; missing escapes or markup?
    37 |   where \eqn{N_{ij}} denotes the number of times that the error profile \eqn{i} is cited on a report from hospital {j} and \eqn{y_{ij}} is the corresponding number of times that profile \eqn{i} in hospital \eqn{j} was reported with harm.
       |                                                                                                                    ^
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) strings-internal.Rd:14: Lost braces
    14 | code{stringPlaceExact}: find location of string, using exact match
       |     ^
checkRd: (-1) strings-internal.Rd:17: Lost braces
    17 | code{stringPlaceFuzzy}: find location of string, using partial match
       |     ^
checkRd: (-1) strings-internal.Rd:19: Lost braces
    19 | code{stringPlace}: find location of string, generic
       |     ^
checkRd: (-1) strings-internal.Rd:21: Lost braces
    21 | code{checkFuzzy}: check for "close" string matches
       |     ^
Packages required but not available:
  'medfate', 'meteoland', 'Rcpp', 'sf', 'shiny', 'stars', 'terra',
  'tidyterra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'meteoland', 'Rcpp', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Packages suggested but not available for checking: 'arm', 'glmnet', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppNumerical', 'flextable', 'shiny', 'shinydashboard',
  'shinyMatrix', 'lme4', 'lmerTest', 'pbkrtest', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'flextable', 'pander'
Error(s) in re-building vignettes:
  ...
--- re-building ‘adjusted-pvalues.Rmd’ using rmarkdown
--- finished re-building ‘adjusted-pvalues.Rmd’

--- re-building ‘case-studies.Rmd’ using rmarkdown

Quitting from lines 661-670 [unnamed-chunk-1] (case-studies.Rmd)
Error: processing vignette 'case-studies.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘case-studies.Rmd’

--- re-building ‘mediana.Rmd’ using rmarkdown
--- finished re-building ‘mediana.Rmd’

SUMMARY: processing the following file failed:
  ‘case-studies.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mediation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘learnr’
Packages required but not available: 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘tm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘MedLEA.Rmd’ using rmarkdown

Quitting from lines 23-41 [example3] (MedLEA.Rmd)
Error: processing vignette 'MedLEA.Rmd' failed with diagnostics:
there is no package called 'tm'
--- failed re-building ‘MedLEA.Rmd’

SUMMARY: processing the following file failed:
  ‘MedLEA.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) MED.Rd:25: Lost braces
    25 | The vector of treatment assignments of length \eqn{n}. Must be coded as \eqn{\{0,1} {{0,1}}.
       |                                                                                     ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘bib2df’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'HDMT', 'qvalue'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tensorMiss’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SKAT', 'pedgene', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'reshape', 'ggrepel', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'dqrng', 'RcppEigen'

Packages suggested but not available for checking: 'car', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'reticulate', 'Rcpp', 'shiny', 'shinyjs', 'leaflet',
  'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinyWidgets', 'shinyBS', 'shinyjs',
  'DT', 'plotly', 'mem'

Packages suggested but not available for checking: 'openxlsx', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magick’

Package suggested but not available for checking: ‘ggimage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinycssloaders', 'shinyBS', 'colourpicker'

Package suggested but not available for checking: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'gdistance', 'raster'

Packages suggested but not available for checking: 'adegenet', 'geosphere'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'AER', 'car', 'lme4'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'forecast', 'LongMemoryTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ranger', 'HH'

Packages suggested but not available for checking:
  'devtools', 'virtualPollen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppRoll’

Package suggested but not available for checking: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'glmnet', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Thresher', 'Rtsne', 'umap', 'kohonen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shiny.i18n', 'shinyjs', 'shinyFiles', 'waiter'

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: 'DT', 'devtools'
Error(s) in re-building vignettes:
  ...
--- re-building ‘mergingTools-vignette.Rmd’ using rmarkdown

Quitting from lines 28-33 [unnamed-chunk-3] (mergingTools-vignette.Rmd)
Error: processing vignette 'mergingTools-vignette.Rmd' failed with diagnostics:
there is no package called 'DT'
--- failed re-building ‘mergingTools-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘mergingTools-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘OpenMx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'lme4', 'shiny', 'blme'

Packages suggested but not available for checking:
  'rstanarm', 'Amelia', '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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'glmnet', 'RcppArmadillo'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rapportools', 'gt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyBS'

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'ggvis', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rstan’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggfittext', 'ggimage', 'meta'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'C50', 'caret', 'InterpretMSSpectrum', 'pcaMethods', 'plyr'

Packages suggested but not available for checking:
  'mixOmics', 'ropls', 'xcms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'factoextra', 'dbscan', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘compareDF’

Packages suggested but not available for checking:
  'metaumbrella', 'TOSTER', 'epiR', 'meta', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Packages suggested but not available for checking:
  'ape', 'lme4', 'meta', 'netmeta'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'reshape2'

Package suggested but not available for checking: ‘pander’

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: 'metadynminer', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'plyr', 'RcppArmadillo'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'minqa', 'lbfgsb3c', 'Epi', 'glmmTMB', 'ape'
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 suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘ape’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'emdbook', 'ggrepel', 'ks', 'Rfast', 'yarrr'

Package suggested but not available for checking: ‘DT’

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.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘meta’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) asympVar_LinReg.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LinReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) asympVar_LogReg.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_gamma_EB.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dataone', 'EML', 'emld'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Package suggested but not available for checking: ‘rasterVis’

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: ‘DescTools’
Package suggested but not available for checking: ‘gt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘adam-mapping.Rmd’ using rmarkdown
--- finished re-building ‘adam-mapping.Rmd’

--- re-building ‘ar-grid.Rmd’ using rmarkdown

Quitting from lines 126-131 [unnamed-chunk-10] (ar-grid.Rmd)
Error: processing vignette 'ar-grid.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘ar-grid.Rmd’

--- re-building ‘component.Rmd’ using rmarkdown
--- finished re-building ‘component.Rmd’

--- re-building ‘metalite.Rmd’ using rmarkdown
--- finished re-building ‘metalite.Rmd’

--- re-building ‘mockup-table.Rmd’ using rmarkdown
--- finished re-building ‘mockup-table.Rmd’

SUMMARY: processing the following file failed:
  ‘ar-grid.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'plyr', 'metagenomeSeq', 'DESeq2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'openxlsx', 'ggrepel', 'qvalue'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'shiny', 'miniUI', 'sf'
Packages required but not available:
  'meta', 'lme4', 'plyr', 'lmerTest', 'compositions'

Packages suggested but not available for checking:
  'repmis', 'reshape2', 'caret', 'tsibble'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'plyr', 'pROC'

Packages suggested but not available for checking: 'ggmcmc', 'logistf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'reshape2', 'pcutils'

Packages suggested but not available for checking:
  'ggraph', 'ggpmisc', 'ggtree', 'treeio', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'ggimage'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'tm', 'textstem'

Package suggested but not available for checking: ‘wordcloud’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GGally', 'ggforce', 'ggrepel', 'lme4', 'lmerTest'

Package suggested but not available for checking: ‘DT’

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: 'fastGHQuad', 'lme4', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘qqconf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ade4', 'ggforce', 'ggrepel', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'terra', '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: 'netmeta', 'pimeta'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘meta’

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DESeq2’
checkRd: (-1) param.Rd:29: Lost braces
    29 | T. Strub, S. Giuliano, T. Ye, et al. (2011) Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma. emph{Oncogene} \bold{30}:2319-32.
       |                                                                                                                                                                       ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘OpenMx’

Package suggested but not available for checking: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘meta’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SKAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'StanHeaders', 'RcppEigen'

Package suggested but not available for checking: ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘meta’

Packages suggested but not available for checking: 'spelling', 'DT', 'epiR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'metaSEM', 'mice'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘KODAMA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

Packages suggested but not available for checking: 'sf', 'rasterVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'stars', 'Rcpp', 'units', 'ncdfgeom'

Packages suggested but not available for checking: 'meteospain', 'worldmet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DescTools', 'caret', 'gstat', 'plyr', 'units', 'nabor', 'CAST',
  'ranger', 'sf', 'sftime', 'raster', 'terra'

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: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'units'

Package suggested but not available for checking: ‘ggforce’

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 suggested but not available for checking: ‘lme4’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'estimatr', 'lme4', 'rockchalk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyFeedback', 'shinyalert', 'DT', 'shinyjs',
  'DoE.wrapper', 'shinyBS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Packages required but not available: 'minerva', 'energy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'rSPDE', 'Rcpp', 'RcppEigen'

Packages suggested but not available for checking:
  'INLA', 'inlabru', 'osmdata', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'plyr', 'sf'

Packages suggested but not available for checking:
  'reshape2', 'terra', 'gsignal', 'rnaturalearth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'shiny', 'shinythemes'

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: 'prodlim', 'icenReg'

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:
  'mvPot', 'revdbayes', 'TruncatedNormal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lamW’

Package suggested but not available for checking: ‘rstpm2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'devtools', 'ggpubr', 'lme4', 'lmerTest'

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:
  'ade4', 'ape', 'betapart', 'FactoMineR', 'gawdis', 'geometry',
  'ggrepel', 'reshape2', 'rstatix'

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: 'tsDyn', 'forecast'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'funData', 'plyr'

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RcppArmadillo’
Note: skipping ‘MfUSampler.Rnw’ due to unavailable dependencies:
  'RcppArmadillo'
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘lmomco’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'energy', 'raster'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qgam', 'gamm4', 'GGally', 'plyr', 'shiny', 'miniUI'

Package suggested but not available for checking: ‘webshot2’

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: ‘MGDrivE’
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV.Rd:81: Lost braces; missing escapes or markup?
    81 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       | ^
checkRd: (-1) summarize_stats_CSV_decoupled.Rd:84: Lost braces; missing escapes or markup?
    84 | {stage}\emph{Mean}(patchNum).csv and {stage}\emph{Quantile}(quantNum)_(patchNum).csv.
       |                                      ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggrepel', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mvabund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'plyr', 'reshape2'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'mvnfast', 'plyr', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

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: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'leaflet', 'sf', 'nabor', 'mapview', 'caret', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'manifold', 'distory', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'imp4p', 'mice'

Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcalg', 'mice', 'Rfast'

Package suggested but not available for checking: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mice', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'BIFIEsurvey', 'blme', 'car', 'CDM', 'lme4', 'MBESS', 'MCMCglmm',
  'mdmb', 'sirt', 'synthpop', 'TAM'

Packages which this enhances but not available for checking:
  'Amelia', 'imputeR', 'jomo', 'micemd', 'mitml', 'simputation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pROC', 'mice', 'mitml', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'micEcon', 'systemfit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'systemfit', 'micEcon'

Package suggested but not available for checking: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sfaR’

Package suggested but not available for checking: ‘micEcon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Ecdat', 'micEcon'
Package required but not available: ‘plm’

Packages suggested but not available for checking: 'Ecdat', 'systemfit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘systemfit’

Package suggested but not available for checking: ‘micEcon’

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: 'mice', 'UpSetR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mice', 'lme4', 'jomo', 'GJRM'

Package suggested but not available for checking: ‘VIM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'ggpubr', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'mitml', 'Rcpp'

Packages suggested but not available for checking:
  'lme4', 'miceadds', 'ranger', 'rstan'

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: 'MVN', 'devtools'
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [12s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2016 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(testthat)
  > 
  > test_check("micompr")
  Loading required package: micompr
  [ FAIL 2 | WARN 73 | SKIP 0 | PASS 291 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_cmpoutput.R:214:3'): assumptions.cmpoutput creates the correct object ──
  <subscriptOutOfBoundsError/error/condition>
  Error in ``*tmp*`[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   1. ├─micompr::assumptions(cmp) at test_cmpoutput.R:214:3
   2. └─micompr:::assumptions.cmpoutput(cmp)
  ── Error ('test_micomp.R:281:3'): micomp assumptions have the correct properties ──
  <subscriptOutOfBoundsError/error/condition>
  Error in ``*tmp*`[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   1. ├─micompr::assumptions(mic1a) at test_micomp.R:281:3
   2. └─micompr:::assumptions.micomp(mic1a)
   3.   └─base::lapply(obj, function(x) assumptions(x))
   4.     └─micompr (local) FUN(X[[i]], ...)
   5.       ├─micompr::assumptions(x)
   6.       └─micompr:::assumptions.cmpoutput(x)
  
  [ FAIL 2 | WARN 73 | SKIP 0 | PASS 291 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘paper.Rnw’ using knitr

Quitting from lines 341-342 [sunspot3] (paper.Rnw)
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘paper.Rnw’

--- re-building ‘tolatex-examples.Rnw’ using knitr
--- finished re-building ‘tolatex-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘paper.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'plyr', 'phyloseq', 'ggpubr', 'DESeq2', 'rstatix', 'phangorn'

Package suggested but not available for checking: ‘dada2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survminer', 'glmnet', 'microbiome'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'microseq', 'microcontax', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘microseq’

Package suggested but not available for checking: ‘microcontax.data’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstatix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'reshape2'

Packages suggested but not available for checking:
  'GUniFrac', 'ggpubr', 'ggrepel', 'picante', 'rgexf', 'mice', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'shiny', 'shinyBS', 'shinyWidgets', 'ggiraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘units’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'spdep', 'rmapshaper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plumber’
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MicroMoB)
  > 
  > test_check("MicroMoB")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1020 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-api_mosquitoes_plumber.R:5:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'plumber'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-api_mosquitoes_plumber.R:5:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1020 ]
  Error: Test failures
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘microseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'HH', 'flextable'

Packages suggested but not available for checking:
  'reshape2', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘emayili’
Package required but not available: ‘survey’

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:
  'AER', 'censReg', 'sampleSelection'
Packages required but not available: 'caret', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mice’
'LazyData' is specified without a 'data' directory
Running examples in ‘midastouch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mice.impute.midastouch
> ### Title: Predictive Mean Matching with distance aided selection of donors
> ### Aliases: mice.impute.midastouch midastouch
> ### Keywords: mice
> 
> ### ** Examples
> 
> ## from R:: mice, slightly adapted ##
> 
> # do default multiple imputation on a numeric matrix
> library(midastouch)
> library(mice)
Error in library(mice) : there is no package called ‘mice’
Execution halted
Packages suggested but not available for checking: 'mice', 'midfielddata'
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'blorr', 'dagitty', 'mice'

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SMR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ranger’
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘manynet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'TruncatedNormal', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘minqa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mi', 'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MIIVsem’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

Package suggested but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gaston', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fuzzyjoin', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'FactoMineR', 'rARPACK'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'DT', 'heatmaply', 'plotly', 'pROC', 'shiny',
  'shinycssloaders', 'shinyFiles', 'shinydashboard', 'shinyjs',
  'shinyWidgets', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘blockmodels’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'JWileymisc', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppEigen'

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:
  'InteractiveComplexHeatmap', 'gsignal', 'mgc', 'mmand'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'testthis', 'spelling'
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘katex’

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', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

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:
  'meta', 'shiny', 'shinyjs', 'shinyWidgets', 'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gof.estimates.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gof.estimates.Rd:63-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gof.estimates.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:63-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vcov.mipfp.Rd:92-95: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shinyWidgets', 'shiny.i18n', 'shinyalert', 'shiny', 'reshape',
  'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘promises’
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘COMPoissonReg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'cubature', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'openxlsx', 'plotly', 'tidytext', 'topicmodels', 'wordcloud'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GUniFrac', 'lme4', 'mixtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pROC', 'qpdf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RSpectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mirt', 'shiny', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘shinythemes’

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', 'dcurver', 'RcppArmadillo'

Packages suggested but not available for checking:
  'latticeExtra', 'shiny', 'sirt', 'mirtCAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mirtjml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mice’
Error(s) in re-building vignettes:
  ...
--- re-building ‘misaem.Rmd’ using rmarkdown

Quitting from lines 60-68 [unnamed-chunk-3] (misaem.Rmd)
Error: processing vignette 'misaem.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building ‘misaem.Rmd’

SUMMARY: processing the following file failed:
  ‘misaem.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘mixAK’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phyloseq', 'dada2', 'ape'

Packages suggested but not available for checking:
  'adespatial', 'ANCOMBC', 'DESeq2', 'devtools', 'DT', 'ggfittext',
  'ggstatsplot', 'gtsummary', 'iNEXT', 'mia', 'mixtools', 'phangorn',
  'phyloseqGraphTest', 'plotly', 'plyr', 'reshape2', 'rotl', 'Rtsne',
  'seqinr', 'SRS', 'treemapify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Ecdat’
checkRd: (-1) sumKeepAttr.Rd:19: Lost braces
    19 |       (only relevant if code{x} has only one element).}
       |                             ^
Running examples in ‘miscTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: colMedians
> ### Title: Medians of Columns
> ### Aliases: colMedians
> ### Keywords: array
> 
> ### ** Examples
> 
>    data( "Electricity", package = "Ecdat" )
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘Ecdat’
Calls: data -> find.package
Execution halted
Running ‘colMediansTest.R’ [0s/0s]
  Running ‘ddnormTest.R’ [0s/0s]
  Comparing ‘ddnormTest.Rout’ to ‘ddnormTest.Rout.save’ ... OK
  Running ‘insertColRow.R’ [0s/0s]
  Comparing ‘insertColRow.Rout’ to ‘insertColRow.Rout.save’ ... OK
  Running ‘lmMethods.R’ [0s/1s]
  Comparing ‘lmMethods.Rout’ to ‘lmMethods.Rout.save’ ... OK
  Running ‘margEffTest.R’ [0s/0s]
  Comparing ‘margEffTest.Rout’ to ‘margEffTest.Rout.save’ ... OK
  Running ‘semidefTest.R’ [0s/0s]
  Comparing ‘semidefTest.Rout’ to ‘semidefTest.Rout.save’ ... OK
  Running ‘stdErTests.R’ [0s/0s]
  Comparing ‘stdErTests.Rout’ to ‘stdErTests.Rout.save’ ... OK
  Running ‘sumKeepAttrTest.R’ [0s/0s]
  Comparing ‘sumKeepAttrTest.Rout’ to ‘sumKeepAttrTest.Rout.save’ ... OK
  Running ‘summarizeDF_tests.R’ [0s/0s]
  Comparing ‘summarizeDF_tests.Rout’ to ‘summarizeDF_tests.Rout.save’ ... OK
Running the tests in ‘tests/colMediansTest.R’ failed.
Complete output:
  > library( "miscTools" )
  > 
  > 
  > ## matrix
  > m <- matrix( 1:24, nrow = 6, ncol = 4 )
  > 
  > cm1 <- colMedians( m )
  > print( cm1 )
  [1]  3.5  9.5 15.5 21.5
  > 
  > rm1 <- rowMedians( m )
  > print( rm1 )
  [1] 10 11 12 13 14 15
  > 
  > all.equal( cm1, rowMedians( t( m ) ) )
  [1] TRUE
  > all.equal( rm1, colMedians( t( m ) ) )
  [1] TRUE
  > 
  > 
  > ## data.frame
  > data( "Electricity", package = "Ecdat" )
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'Ecdat'
  Calls: data -> find.package
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘mice’
Error(s) in re-building vignettes:
  ...
--- re-building ‘miselect.Rmd’ using rmarkdown

Quitting from lines 76-82 [unnamed-chunk-4] (miselect.Rmd)
Error: processing vignette 'miselect.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building ‘miselect.Rmd’

SUMMARY: processing the following file failed:
  ‘miselect.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'shiny'

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: 'ape', 'aSPU', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘ade4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Amelia', 'mi', 'mice', 'missMDA', 'pcaMethods', 'plyr', 'VIM'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'factoextra', 'Rcpp', 'glmnet', 'sparsevar', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'relsurv', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mice’
Running examples in ‘missDiag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: missDiag
> ### Title: Comparing Observed and Imputed Values under MAR and MCAR
> ### Aliases: missDiag
> 
> ### ** Examples
> 
> 
> # Compare random value imputation 
> # with predictive mean imputation 
> # under MCAR
> 
> diag_rng <- missDiag( 
+  original=anes08, 
+  imputed=anes08_rng, 
+  verbose = 1,
+  adjust = 'none',
+  formula = time ~ .)
Error in loadNamespace(x) : there is no package called ‘mice’
Calls: missDiag ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘imputeTS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpubr', 'ggmcmc', 'BCEA', 'bayesplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', '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', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'SIS', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'sbm', 'RSpectra', 'RcppArmadillo'

Packages suggested but not available for checking:
  'aricode', 'blockmodels', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘KrigInv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'mice', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'tigris'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘jomo’

Packages suggested but not available for checking:
  'mice', 'miceadds', 'Amelia', 'lme4', 'glmmTMB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rdist', 'reshape2'

Packages suggested but not available for checking:
  'clustree', 'karyoploteR', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) PV.Rd:14: Lost braces
    14 | plausible value in turn; with code{rewrite=FALSE} a new data set is
       |                                   ^
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘animation’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'GGally', 'mice', 'pander', 'spelling'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'fastGHQuad'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rtkore', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fma’
Running examples in ‘mixAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MixARGaussian-class
> ### Title: mixAR models with Gaussian noise components
> ### Aliases: MixARGaussian-class MixARGaussian
> ### Keywords: classes MixAR
> 
> ### ** Examples
> 
> showClass("MixARGaussian")
Class "MixARGaussian" [package "mixAR"]

Slots:
                                                             
Name:        prob      order      shift      scale     arcoef
Class:    numeric    numeric    numeric    numeric raggedCoef

Extends: "MixAR"
> 
> ## load ibm data from BJ
> ## data(ibmclose, package = "fma")
> 
> ## compute a predictive density, assuming exampleModels$WL_ibm model
> ## for the first date after the end of the data
> pdf1 <- mix_pdf(exampleModels$WL_ibm, xcond = as.numeric(fma::ibmclose))
Error in (function (cond)  : 
  error in evaluating the argument 'xcond' in selecting a method for function 'mix_pdf': there is no package called ‘fma’
Calls: mix_pdf ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
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Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'flexsurv', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'fMultivar', 'latentcor', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'scran', 'Seurat', 'scuttle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Packages required but not available: 'mixOmics', 'reticulate', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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: ‘meta’
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘splitfngr’

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  'ContourFunctions', 'lhs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'ggrepel'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mixRasch’
Skipping checking math rendering: package 'V8' unavailable
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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: ‘mixtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape', 'reshape2', 'ggmcmc', 'bayesplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pROC', '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
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  'ggrepel', 'plotly', 'plyr', 'Rcpp', '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:
  'funData', 'gamm4', 'refund', 'fdapace', 'sparseFLMM', 'MFPCA',
  'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'sf', 'terra', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package required but not available: ‘miceadds’

Packages suggested but not available for checking: 'Amelia', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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Package suggested but not available for checking: ‘Amelia’
Running examples in ‘MKmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mi.t.test
> ### Title: Multiple Imputation Student's t-Test
> ### Aliases: mi.t.test mi.t.test.default
> ### Keywords: htest
> 
> ### ** Examples
> 
> ## Generate some data
> set.seed(123)
> x <- rnorm(25, mean = 1)
> x[sample(1:25, 5)] <- NA
> y <- rnorm(20, mean = -1)
> y[sample(1:20, 4)] <- NA
> pair <- c(rnorm(25, mean = 1), rnorm(20, mean = -1))
> g <- factor(c(rep("yes", 25), rep("no", 20)))
> D <- data.frame(ID = 1:45, variable = c(x, y), pair = pair, group = g)
> 
> ## Use Amelia to impute missing values
> library(Amelia)
Error in library(Amelia) : there is no package called ‘Amelia’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'MKinfer', 'qqplotr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'keras', 'reticulate', 'tensorflow', 'tfprobability'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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Packages suggested but not available for checking: 'ggtext', 'gridtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'ConfusionTableR', 'recipes', 'ranger', 'caret', 'OddsPlotty'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Packages required but not available:
  'bivpois', 'Compositional', 'Directional', 'geppe', 'gp', 'MN',
  'Rfast', 'Rfast2'

Package suggested but not available for checking: ‘mvcauchy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'reshape2', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Skipping checking math rendering: package 'V8' unavailable
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DESCRIPTION file?
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘httpuv’

Packages suggested but not available for checking: 'keras', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ranger', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
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  'glmnet', 'ParBayesianOptimization', 'quarto', 'ranger'

VignetteBuilder package required for checking but not installed: ‘quarto’
Running examples in ‘mllrnrs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LearnerGlmnet
> ### Title: R6 Class to construct a Glmnet learner
> ### Aliases: LearnerGlmnet
> 
> ### ** Examples
> 
> # binary classification
> 
> library(mlbench)
> data("PimaIndiansDiabetes2")
> dataset <- PimaIndiansDiabetes2 |>
+   data.table::as.data.table() |>
+   na.omit()
> 
> seed <- 123
> feature_cols <- colnames(dataset)[1:8]
> 
> train_x <- model.matrix(
+   ~ -1 + .,
+   dataset[, .SD, .SDcols = feature_cols]
+ )
> train_y <- as.integer(dataset[, get("diabetes")]) - 1L
> 
> fold_list <- splitTools::create_folds(
+   y = train_y,
+   k = 3,
+   type = "stratified",
+   seed = seed
+ )
> glmnet_cv <- mlexperiments::MLCrossValidation$new(
+   learner = mllrnrs::LearnerGlmnet$new(
+     metric_optimization_higher_better = FALSE
+   ),
+   fold_list = fold_list,
+   ncores = 2,
+   seed = 123
+ )
Error: Package "glmnet" must be installed to use 'learner = "LearnerGlmnet"'.
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'lme4', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bootImpute’
checkRd: (-1) refBasedCts.Rd:44: Lost braces
    44 | using reference based imputation as proposed by \doi{10.1080/10543406.2013.834911}{Carpenter et al (2013)}. This approach
       |                                                                                   ^
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
Package required but not available: ‘sommer’

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.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lmerTest', 'varTestnlme'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'quantspec', 'Rfast', 'TSclust', 'forecast', 'tsfeatures', 'MTS',
  'fda.usc', 'TSdist', 'DescTools', 'ClusterR', 'AID', 'caret',
  'ranger'

Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'car', 'AER'
Running examples in ‘mlogit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmftest
> ### Title: Hausman-McFadden Test
> ### Aliases: hmftest hmftest.formula hmftest.mlogit
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> ## from Greene's Econometric Analysis p. 731
> 
> data("TravelMode", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Running ‘AER.R’ [0s/1s]
  Running ‘greene.R’ [1s/2s]
Running the tests in ‘tests/AER.R’ failed.
Complete output:
  > # BankWages.Rd
  > 
  > library("lmtest")
  Loading required package: zoo
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  > data("BankWages", package = "AER")
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'AER'
  Calls: data -> find.package
  Execution halted
Running the tests in ‘tests/greene.R’ failed.
Complete output:
  > library("mlogit")
  Loading required package: dfidx
  
  Attaching package: 'dfidx'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > data("TravelMode", package = "AER")
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'AER'
  Calls: data -> find.package
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'RcppEnsmallen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘C50’
Packages suggested but not available for checking:
  'lme4', 'lmerTest', 'mirt', 'simr'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘PMCMRplus’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'apcluster', 'ClusterR', 'dbscan', 'stream'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'ranger', 'posterdown', 'fairml'
checkRd: (-1) groupdiff_tau.Rd:23: Lost braces
    23 | \code{groupdiff_tau()} computes \eqn{min(x/y, y/x)}, i.e. the smallest symmetric ratio between \eqn{x} and eqn{y}
       |                                                                                                               ^
Running examples in ‘mlr3fairness-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fairness_accuracy_tradeoff
> ### Title: Plot Fairness Accuracy Trade-offs
> ### Aliases: fairness_accuracy_tradeoff
> 
> ### ** Examples
> 
> library("mlr3")
> library("mlr3learners")
> library("ggplot2")
> 
> # Setup the Fairness measure and tasks
> task = tsk("adult_train")$filter(1:500)
> learner = lrn("classif.ranger", predict_type = "prob")
Warning: Package 'ranger' required but not installed for Learner 'classif.ranger'
> fairness_measure = msr("fairness.tpr")
> 
> # Example 1 - A single prediction
> learner$train(task)
Error: The following packages could not be loaded: ranger
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'Boruta', 'caret', 'carSurv', 'FSelectorRcpp'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'glmnet', 'ranger'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘spacefillr’

Packages suggested but not available for checking:
  'fastGHQuad', 'lhs', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘qs’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'glmnet', 'lme4', 'quanteda', 'bestNormalize', 'smotefamily', 'NMF',
  'ranger', 'themis'
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Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘animint2’
Packages required but not available:
  'shiny', 'shinydashboard', 'shinyjs', 'shinyWidgets', 'shinyalert',
  'DT', 'plyr'

Packages suggested but not available for checking:
  'shinytest', 'devtools', 'ranger'

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:
  'ranger', 'raster', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'blockCV', 'caret', 'CAST', 'ggtext', 'mlr3spatial', 'plotly', 'sf',
  'terra'
Running examples in ‘mlr3spatiotempcv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mlr_resamplings_repeated_spcv_knndm
> ### Title: (CAST) Repeated K-fold Nearest Neighbour Distance Matching
> ### Aliases: mlr_resamplings_repeated_spcv_knndm
> ###   ResamplingRepeatedSpCVKnndm
> 
> ### ** Examples
> 
> library(mlr3)
> library(mlr3spatial)
Error in library(mlr3spatial) : there is no package called ‘mlr3spatial’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mlr3spatiotempcv.Rmd’ using rmarkdown

Quitting from lines 51-56 [08-special-spatiotemp-002] (mlr3spatiotempcv.Rmd)
Error: processing vignette 'mlr3spatiotempcv.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘mlr3spatiotempcv.Rmd’

--- re-building ‘spatiotemp-viz.Rmd’ using rmarkdown

Quitting from lines 90-148 [unnamed-chunk-4] (spatiotemp-viz.Rmd)
Error: processing vignette 'spatiotemp-viz.Rmd' failed with diagnostics:
The following packages could not be loaded: sf,ggtext
--- failed re-building ‘spatiotemp-viz.Rmd’

SUMMARY: processing the following files failed:
  ‘mlr3spatiotempcv.Rmd’ ‘spatiotemp-viz.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'fastshap', 'ranger'
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘torch’

Packages suggested but not available for checking: 'magick', 'torchvision'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mlflow’
Packages suggested but not available for checking: 'glmnet', 'ranger'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mlr3mbo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GGally', 'glmnet', 'precrec', 'ranger'
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'ranger', 'Rfast', 'FSelectorRcpp'
Package required but not available: ‘lhs’

Packages suggested but not available for checking:
  'cmaesr', 'smoof', 'mlrMBO', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smoof', 'lhs'

Packages suggested but not available for checking:
  'cmaesr', 'GGally', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'adabag', 'C50', 'caret', 'ClusterR', 'clusterSim', 'crs', 'Cubist',
  'fda.usc', 'forecast', 'FSelectorRcpp', 'ggpubr', 'glmnet', 'GPfit',
  'klaR', 'mldr', 'mlrMBO', 'pander', 'pec', 'penalized', 'PMCMRplus',
  'ranger', 'refund', 'RSNNS', 'rucrdtw', 'sf', 'smoof', 'tsfeatures'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘madshapR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'glmnet', 'ParBayesianOptimization', 'quarto', 'ranger'

VignetteBuilder package required for checking but not installed: ‘quarto’
Running examples in ‘mlsurvlrnrs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LearnerSurvCoxPHCox
> ### Title: R6 Class to construct a Cox proportional hazards survival
> ###   learner
> ### Aliases: LearnerSurvCoxPHCox
> 
> ### ** Examples
> 
> # survival analysis
> 
> dataset <- survival::colon |>
+   data.table::as.data.table() |>
+   na.omit()
> dataset <- dataset[get("etype") == 2, ]
> 
> seed <- 123
> surv_cols <- c("status", "time", "rx")
> 
> feature_cols <- colnames(dataset)[3:(ncol(dataset) - 1)]
> 
> split_vector <- splitTools::multi_strata(
+   df = dataset[, .SD, .SDcols = surv_cols],
+   strategy = "kmeans",
+   k = 4
+ )
> 
> train_x <- model.matrix(
+   ~ -1 + .,
+   dataset[, .SD, .SDcols = setdiff(feature_cols, surv_cols[1:2])]
+ )
> train_y <- survival::Surv(
+   event = (dataset[, get("status")] |>
+              as.character() |>
+              as.integer()),
+   time = dataset[, get("time")],
+   type = "right"
+ )
> 
> fold_list <- splitTools::create_folds(
+   y = split_vector,
+   k = 3,
+   type = "stratified",
+   seed = seed
+ )
> 
> 
> surv_coxph_cox_optimizer <- mlexperiments::MLCrossValidation$new(
+   learner = LearnerSurvCoxPHCox$new(),
+   fold_list = fold_list,
+   ncores = 1L,
+   seed = seed
+ )
> surv_coxph_cox_optimizer$performance_metric <- c_index
> 
> # set data
> surv_coxph_cox_optimizer$set_data(
+   x = train_x,
+   y = train_y
+ )
> 
> surv_coxph_cox_optimizer$execute()

CV fold: Fold1
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.

CV fold: Fold2
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.

CV fold: Fold3
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.
Error in mlr3measures::measures[[fun_name]] : 
  wrong arguments for subsetting an environment
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Packages required but not available: 'mlt', 'flexsurv'

Packages suggested but not available for checking:
  'prodlim', 'latticeExtra', 'AER', 'tram'

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.
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  'pdftools', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  'lme4', 'arm', 'qgraph', 'plyr', 'MplusAutomation', 'graphicalVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking:
  'ggforce', 'spelling', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Rcpp', 'reshape2', 'shiny'
checkRd: (-1) simpopmlx.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fim}{the Fisher Information Matrix estimated by Monolix. fim={"sa", "lin"} (default="sa")}
       |                                                                    ^
Packages required but not available: 'reshape2', 'TMB', 'RcppEigen'

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: 'glmnet', 'mma', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mosaicCalc’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'leaflet', 'shiny', 'shinyjs', 'plotly'

Packages suggested but not available for checking: 'devtools', 'shinytest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'refund', 'cosinor', 'cosinor2', 'accelerometry', 'ActCR', 'ActFrag',
  'GGIR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'caret', 'ggpubr', 'philentropy', 'Rtsne'
'LazyData' is specified without a 'data' directory
Running ‘helpers.R’ [0s/1s]
  Running ‘testthat.R’ [46s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mmb)
  > 
  > test_check("mmb")
  [ FAIL 2 | WARN 139 | SKIP 0 | PASS 327 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_bayes.R:354:3'): the full Bayesian works with many variables ───
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'caret'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_bayes.R:354:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_bayes.R:431:3'): assigning for multiple works using naive Bayes ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'caret'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_bayes.R:431:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 139 | SKIP 0 | PASS 327 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Cluster-Analysis.rmd’ using rmarkdown

Quitting from lines 26-95 [unnamed-chunk-1] (Cluster-Analysis.rmd)
Error: processing vignette 'Cluster-Analysis.rmd' failed with diagnostics:
there is no package called 'Rtsne'
--- failed re-building ‘Cluster-Analysis.rmd’

SUMMARY: processing the following file failed:
  ‘Cluster-Analysis.rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'psqn'

Package suggested but not available for checking: ‘mets’

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: 'devtools', 'qtl2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘simstudy’
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown

Quitting from lines 21-25 [setup] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'simstudy'
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'cubature', 'wdm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'bigmemory'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) mmeln.Rd:69: Lost braces; missing escapes or markup?
    69 |   \item{obj$M}{Number of total observations sum_{i=1}^N(pi)}
       |                                                 ^
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GFM', 'MultiCOAP', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'DT', 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clusterSEs', 'DT', 'lmerTest', 'pool', 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DT', 'pool', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'pool', 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Spectrum’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caper', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'adegenet', 'pegas'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'RcppEigen', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) k2d.Rd:26: Lost braces
    26 | d_ND(x,y) = sqrt{ k(x,x) - 2k(x,y) + k(y,y)}.
       |                 ^
checkRd: (-1) k2d.Rd:34: Lost braces
    34 | d_n(x,y) = 1 - k(x,y)/sqrt{ k(x,x)k(y,y)},
       |                           ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'TMB', 'RcppEigen'

Packages suggested but not available for checking:
  'car', 'glmmTMB', 'lme4', 'sasr', 'tidymodels'

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 required but not available: 'reticulate', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'reshape', 'reshape2', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'keras', 'tensorflow', 'reticulate', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlVAR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CDM', 'Rcpp', 'RcppArmadillo'

Packages which this enhances but not available for checking:
  'aMNLFA', 'GPCMlasso', 'sirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ICSNP', 'ICS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'hpa', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'DT'
checkRd: (-1) mom.mtruncnorm.Rd:35: Lost braces
    35 |   \item{cum}{a logical value; if  code{TRUE}  (default value), cumulants 
       |                                       ^
checkRd: (-1) mom.mtruncnorm.Rd:43: Lost braces; missing escapes or markup?
    43 | The maximal value of {d} is \code{20}. If this threshold is exceeded, \code{NA}s
       |                      ^
checkRd: (-1) mt.Rd:110: Lost braces
   110 |   and code{tvpack}, downloaded in 2005 and again in 2007 from his webpage, 
       |           ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'sommer', 'vcfR', 'optiSel', 'alstructure', 'NAM', 'phylogram',
  'cPCG'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
checkRd: (-1) creating.phenotypic.transform.Rd:20: Lost braces
    20 | trafo <- function(x){ return(x^2)}
       |                     ^
Running examples in ‘MoBPS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get.dendrogram
> ### Title: Dendrogram
> ### Aliases: get.dendrogram
> 
> ### ** Examples
> 
> data(ex_pop)
> get.dendrogram(ex_pop, gen=2)
Error in get.dendrogram(ex_pop, gen = 2) : object 'geno_dend' not found
Execution halted
Package required but not available: ‘Rborist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geosphere', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'sads'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggbio', 'wCorr', 'ggrepel', 'qvalue'

Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'chromVAR', 'uwot', 'glmmTMB', 'lmerTest',
  'lme4', 'mixtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'genieclust', 'genio', 'partition'

Package suggested but not available for checking: ‘CCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) lientz.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lientz.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lientz.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘plyr’
Packages suggested but not available for checking:
  'brms', 'gamm4', 'gganimate', 'glmmTMB', 'lme4', 'marginaleffects',
  'rstanarm', 'rtdists'
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'auditor', 'DT', 'archivist', 'devtools'

Packages suggested but not available for checking: 'ranger', 'useful'

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: ‘lme4’
Running examples in ‘modelfactory-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stack_metrics
> ### Title: Combine model metrics for n number of lm, glm, and lmer models
> ### Aliases: stack_metrics
> 
> ### ** Examples
> 
> # lm example -------------------------------------------
> lm_1 = lm(mpg ~ cyl + disp + hp, data = mtcars)
> lm_2 = lm(mpg ~ hp + drat + wt, data = mtcars)
> lm_3 = lm(mpg ~ ., data = mtcars)
> lm_combined = stack_metrics(lm_1, lm_2, lm_3)
> lm_combined
# A tibble: 3 × 6
  model                                r.squared adj.r.squared   MSE  RMSE   MAE
  <chr>                                    <dbl>         <dbl> <dbl> <dbl> <dbl>
1 lm(formula = mpg ~ cyl + disp + hp,…     0.768         0.743  8.17  2.86  2.32
2 lm(formula = mpg ~ hp + drat + wt, …     0.837         0.819  5.74  2.40  1.91
3 lm(formula = mpg ~ ., data = mtcars)     0.869         0.807  4.61  2.15  1.72
> 
> # glm example ------------------------------------------
> glm_1 = glm(vs ~ drat + hp, data = mtcars)
> glm_2 = glm(vs ~ wt + qsec, data = mtcars)
> glm_3 = glm(vs ~ ., data = mtcars)
> glm_combined = stack_metrics(glm_1, glm_2, glm_3)
> glm_combined
# A tibble: 3 × 4
  model                                        deviance   AIC   BIC
  <chr>                                           <dbl> <dbl> <dbl>
1 glm(formula = vs ~ drat + hp, data = mtcars)     3.63  29.1  35.0
2 glm(formula = vs ~ wt + qsec, data = mtcars)     2.04  10.8  16.6
3 glm(formula = vs ~ ., data = mtcars)             1.58  18.6  36.2
> 
> # lme4 example -----------------------------------------
> lmer_1 = lme4::lmer(Sepal.Length ~ (1 | Species), data = iris)
Error in loadNamespace(x) : there is no package called ‘lme4’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(modelfactory)
  > 
  > test_check("modelfactory")
  Waiting for profiling to be done...
  Waiting for profiling to be done...
  Waiting for profiling to be done...
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-combine.R:18:1'): (code run outside of `test_that()`) ──────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-combine.R:18:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘PolynomF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'coxrobust', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'ranger', 'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [73s/79s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("modelStudio")
  > library("DALEX")
  Welcome to DALEX (version: 2.4.3).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  
  Attaching package: 'DALEX'
  
  The following object is masked from 'package:modelStudio':
  
      happiness_train
  
  > requireNamespace("ranger", quietly=TRUE)
  > requireNamespace("xgboost", quietly=TRUE)
  > 
  > test_check("modelStudio")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_modelStudio.R:33:1'): (code run outside of `test_that()`) ──────
  Error in `eval(code, test_env)`: object 'explain_rf' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_silent(...) at test_modelStudio.R:33:1
   2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ ├─withr::with_output_sink(...)
   5. │   │ │ └─base::force(code)
   6. │   │ ├─base::withCallingHandlers(...)
   7. │   │ └─base::withVisible(code)
   8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   9. └─modelStudio::modelStudio(...)
  ── Error ('test_ms_options.R:76:1'): (code run outside of `test_that()`) ───────
  Error in `eval(code, test_env)`: object 'explain_rf' not found
  Backtrace:
      ▆
   1. └─modelStudio::modelStudio(...) at test_ms_options.R:76:1
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 28 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ms-perks-features.Rmd’ using rmarkdown
--- finished re-building ‘ms-perks-features.Rmd’

--- re-building ‘ms-r-python-examples.Rmd’ using rmarkdown
--- finished re-building ‘ms-r-python-examples.Rmd’

--- re-building ‘ms-rmarkdown.Rmd’ using rmarkdown

Quitting from lines 59-75 [unnamed-chunk-1] (ms-rmarkdown.Rmd)
Error: processing vignette 'ms-rmarkdown.Rmd' failed with diagnostics:
there is no package called 'ranger'
--- failed re-building ‘ms-rmarkdown.Rmd’

SUMMARY: processing the following file failed:
  ‘ms-rmarkdown.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'AER', 'altdoc', 'Amelia', 'brms', 'car', 'did', 'DT', 'estimatr',
  'fixest', 'flextable', 'ggdist', 'gt', 'gtExtras', 'ivreg', 'lme4',
  'magick', 'marginaleffects', 'mice', 'openxlsx', 'rstanarm',
  'spelling', 'survey', 'tinysnapshot', 'webshot2'
Packages required but not available:
  'modeltime', 'modeltime.resample', 'tune', 'recipes', 'timetk',
  'glmnet'

Packages suggested but not available for checking: 'gt', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'StanHeaders', 'timetk', 'plotly', 'gt', 'forecast', 'prophet',
  'tidymodels'

Packages suggested but not available for checking:
  'rstan', 'workflowsets', 'recipes', 'tune', 'glmnet', 'thief',
  'smooth', 'greybox', 'qpdf', 'TSrepr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'modeltime', 'tune', 'recipes', 'timetk', 'plotly'

Packages suggested but not available for checking:
  'tidymodels', 'tidyquant', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘metadata.Rmd’ using rmarkdown

Quitting from lines 12-14 [unnamed-chunk-1] (metadata.Rmd)
Error: processing vignette 'metadata.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘metadata.Rmd’

--- re-building ‘missings.Rmd’ using rmarkdown
--- finished re-building ‘missings.Rmd’

--- re-building ‘performance.Rmd’ using rmarkdown
--- finished re-building ‘performance.Rmd’

SUMMARY: processing the following file failed:
  ‘metadata.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'markovchain', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinyBS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'DT', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggcorrplot', 'GLDEX', 'gp'

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: ‘survey’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'sf', 'terra'

Packages suggested but not available for checking: 'mapview', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Running examples in ‘modmarg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: marg.ivreg
> ### Title: Predicted Margins for 'ivreg' objects from the 'AER' package
> ### Aliases: marg.ivreg
> 
> ### ** Examples
> 
> # From ?AER::ivreg
> 
> # data
> data("CigarettesSW", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'glmnet', 'lme4', 'lmerTest', 'plyr', 'qgraph', 'reshape2',
  'systemfit'

Package suggested but not available for checking: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'MplusAutomation', 'mvnfast', 'fastGHQuad', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DescTools', 'C50', 'pROC', 'relaimpo', 'car', 'NeuralNetTools',
  'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages suggested but not available for checking: 'smoof', 'reshape2'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘mvnfast’

Packages suggested but not available for checking: 'clustMD', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘compareDF’

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: 'alphahull', 'Rvcg'

Package suggested but not available for checking: ‘rglwidget’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
Packages required but not available: 'urltools', 'MolgenisAuth'

Package suggested but not available for checking: ‘webmockr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'glmnet', 'sparseMatrixStats', '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:
  'Rcpp', 'crawl', 'raster', 'RcppArmadillo'

Packages suggested but not available for checking:
  'splines2', 'ggmap', 'moveHMM', 'extraDistr', 'geosphere', 'car',
  'prodlim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'geomorph', 'sf'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'tlrmvnmvt', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DT', 'shiny', 'shinyBS'
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
'LazyData' is specified without a 'data' directory
checkRd: (-1) TemplateList-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TemplateList-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TemplateList-class.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TemplateList-class.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TemplateList-class.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bindEvents.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bindEvents.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bindEvents.Rd:28: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'shiny', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'shiny', 'shinydashboard', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mice’
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                       ^
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                               ^
checkRd: (-1) circ_dist.Rd:21: Lost braces; missing escapes or markup?
    21 | The distance between two observations {i} and {j} of a circular variable {q}
       |                                                                          ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'raster', 'rnaturalearth', 'sf', 'shiny', 'shinydashboard',
  'shinythemes', 'shinyWidgets', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ggforce', 'rxode2'

Packages suggested but not available for checking:
  'devtools', 'xgxr', 'lixoftConnectors'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ape', 'phytools', 'phangorn'

Packages suggested but not available for checking: 'paleotree', 'taxize'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) legacy.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) legacy.Rd:40: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
GNU make is a SystemRequirements.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘magick’

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'shinyWidgets', 'shinyMatrix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidytext', 'ggwordcloud', 'anytime'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ztable’
Error(s) in re-building vignettes:
  ...
--- re-building ‘moonBook.Rmd’ using rmarkdown

Quitting from lines 179-185 [unnamed-chunk-18] (moonBook.Rmd)
Error: processing vignette 'moonBook.Rmd' failed with diagnostics:
could not find function "addSigColor"
--- failed re-building ‘moonBook.Rmd’

--- re-building ‘moonBook_update.Rmd’ using rmarkdown

Quitting from lines 82-83 [unnamed-chunk-8] (moonBook_update.Rmd)
Error: processing vignette 'moonBook_update.Rmd' failed with diagnostics:
could not find function "ztable"
--- failed re-building ‘moonBook_update.Rmd’

SUMMARY: processing the following files failed:
  ‘moonBook.Rmd’ ‘moonBook_update.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Rcpp', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggraph’

Packages suggested but not available for checking: 'devtools', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'shiny', 'shinyWidgets', 'rclipboard', 'DT', 'datamods'

Packages suggested but not available for checking: 'caret', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

Package suggested but not available for checking: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cld2’
checkRd: (-1) morphemepiece_cache_dir.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morphemepiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) morphemepiece_cache_dir.Rd:22-24: Lost braces in \itemize; meant \describe ?
Packages required but not available:
  'Arothron', 'Rvcg', 'Morpho', 'oce', 'geometry', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rvcg', 'Rcpp', 'sf', 'RcppArmadillo'

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'concaveman', 'automap', 'alphahull'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ade4', 'candisc', 'car', 'heplots', 'StatMatch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'crch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape2’

Package which this enhances but not available for checking: ‘lifecontingencies’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘plotly’
Packages required but not available: 'calculus', 'metR', 'Ryacas'

Packages suggested but not available for checking: 'cubature', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mosaicCalc’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘reshape2’
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggstance', 'ggrepel', 'latticeExtra', 'leaflet'
Running examples in ‘mosaic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fitSpline
> ### Title: Fit splines to data
> ### Aliases: fitSpline
> 
> ### ** Examples
> 
> f <- fitSpline( weight ~ height, data=women, df=5 )
> xyplot( weight ~ height, data=women )
> plotFun(f(height) ~ height, add=TRUE)
Error in plotFun(f(height) ~ height, add = TRUE) : 
  The package "latticeExtra" is required.
Calls: plotFun -> <Anonymous>
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dbscan', 'Rtsne'

Packages suggested but not available for checking:
  'bigparallelr', 'bigstatsr', 'scatterpie', 'ggpmisc', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MBESS', 'ez', 'reshape'

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:
  'comat', 'philentropy', 'Rcpp', 'sf', 'stars', 'RcppArmadillo'

Packages suggested but not available for checking: 'spdep', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggraph', 'reshape2', 'reticulate'

Package suggested but not available for checking: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'Rcpp', 'ks', 'caper'

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: ‘latticeExtra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘mountainplot_examples.Rmd’ using rmarkdown

Quitting from lines 50-55 [ecdf] (mountainplot_examples.Rmd)
Error: processing vignette 'mountainplot_examples.Rmd' failed with diagnostics:
could not find function "ecdfplot"
--- failed re-building ‘mountainplot_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mountainplot_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘V8’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'cstab', 'fields'

Package suggested but not available for checking: ‘readbulk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'units'

Packages suggested but not available for checking:
  'lwgeom', 's2', 'move', 'raster', 'rnaturalearth', 'gganimate',
  'prettymapr', 'ggspatial'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gdistance', 'elevatr', 'raster', 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggmap', 'magick', 'move', 'raster', 'sf', 'stars', 'starsExtra',
  'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'geosphere', 'ggmap', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘osfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geosphere', 'raster', 'terra', 'Rcpp'

Packages suggested but not available for checking:
  'adehabitatHR', 'adehabitatLT', 'ggmap', 'leaflet', 'ctmm', 'amt',
  'bcpa', 'EMbC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'move', 'Rcpp'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'animation', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘movMF.Rnw’ using Sweave

Error: processing vignette 'movMF.Rnw' failed with diagnostics:
 chunk 12 
Error in library("tm") : there is no package called 'tm'

--- failed re-building 'movMF.Rnw'

SUMMARY: processing the following file failed:
  'movMF.Rnw'

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘treemapify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'RcmdrMisc'

Packages suggested but not available for checking:
  'car', 'glmnet', 'np', 'NeuralNetTools', 'vivid',
  'AppliedPredictiveModeling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking: 'zic', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) thresh.est.Rd:16: Lost braces
    16 |   Calculates the stimulus level(s) for a probit model of a psychometric function for given levels of performance.  For a more general version, see \link[MASS]{dose.p} in pkg{MASS}.
       |                                                                                                                                                                              ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

Package suggested but not available for checking: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bestglm', 'plyr', 'shinydashboard', 'shiny', 'glmnet', 'reshape2'

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MplusAutomation’

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.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'bkmr', 'bws', 'infinitefactor', 'qgcomp', 'rstan', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ape’

Package suggested but not available for checking: ‘caper’

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', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'MPTinR', 'TreeBUGS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plotly', 'UpSetR'

Package suggested but not available for checking: ‘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
Packages required but not available:
  'DescTools', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen',
  'StanHeaders'

Package suggested but not available for checking: ‘MendelianRandomization’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘keras’
Packages required but not available: 'fields', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'fda', 'fdapace', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Packages suggested but not available for checking:
  'ows4R', 'leaflet', 'leaflet.extras2', 'mapview'

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: 'fields', 'glmnet', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'plyr', 'caret', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geometry', 'reshape2', 'Rcpp', 'RcppEigen', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'nnfor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'sf', 'stars', 'plyr'

Packages suggested but not available for checking:
  'giscoR', 'units', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mrgsolve', 'fst'

Package suggested but not available for checking: ‘qs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mrgsolve’

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: ‘pmxTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘IHSEP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘oro.nifti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'Rcpp', 'shinyjs', 'bigmemory', 'mrMLM', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'compositions', 'GGally', 'mice', 'pcalg', 'WGCNA', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) bmi.bmi.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.bmi.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.bmi.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.sbp.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.sbp.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) bmi.sbp.Rd:16: Lost braces in \enumerate; meant \describe ?
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package which this enhances but not available for checking: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) data_binary.Rd:10: Lost braces; missing escapes or markup?
    10 |            log E(Y_{t+1} | A_t = 0, I_t = 1) = alpha_0 + alpha_1 * time / total_T
       |                    ^
Packages required but not available: 'plotly', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) msa-package.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa-package.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa-package.Rd:21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:65: Lost braces in \enumerate; meant \describe ?
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checkRd: (-1) msa.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) msa.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msa.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.msa.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.msa.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) n.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) n.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doconv’
Package required but not available: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GA', 'Rmalschains', 'reshape'
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phangorn', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pander’

Package suggested but not available for checking: ‘mscsweblm4r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pander’

Package suggested but not available for checking: ‘mscstexta4r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘terra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘average-daily.Rmd’ using rmarkdown

Quitting from lines 26-47 [unnamed-chunk-2] (average-daily.Rmd)
Error: processing vignette 'average-daily.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘average-daily.Rmd’

--- re-building ‘raster-sample.Rmd’ using rmarkdown

Quitting from lines 24-32 [unnamed-chunk-2] (raster-sample.Rmd)
Error: processing vignette 'raster-sample.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘raster-sample.Rmd’

--- re-building ‘sample-walkthrough.Rmd’ using rmarkdown

Quitting from lines 28-62 [unnamed-chunk-2] (sample-walkthrough.Rmd)
Error: processing vignette 'sample-walkthrough.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘sample-walkthrough.Rmd’

--- re-building ‘vector-from-raster.Rmd’ using rmarkdown

Quitting from lines 24-33 [unnamed-chunk-1] (vector-from-raster.Rmd)
Error: processing vignette 'vector-from-raster.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘vector-from-raster.Rmd’

SUMMARY: processing the following files failed:
  ‘average-daily.Rmd’ ‘raster-sample.Rmd’ ‘sample-walkthrough.Rmd’
  ‘vector-from-raster.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: 'ggrepel', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'DT', 'openxlsx', 'reshape2', 'shiny', 'TMB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nnfor', 'MSGARCH', 'forecast'

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.
Found the following files/directories:
  ‘test.txt’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘animation’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'reticulate', 'caret'
Packages required but not available: 'do', 'set', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘philentropy’

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', 'fields', '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:
  'plyr', 'caret', 'mice', 'pROC', 'ranger'

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: 'forecast', 'plyr', 'Rssa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Packages required but not available:
  'BayesMallows', 'bmixture', 'factoextra', 'fields', 'Rankcluster',
  'Rcpp', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'minqa', 'flexsurv'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘relsurv’
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: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PP', 'mirt', 'scDIFtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'GA', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'crul', 'shinyjs', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) multivar_joint_shannon_entropy.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
checkRd: (-1) total_correlation.Rd:20: Lost braces
    20 |     {\code{table.variables}, \code{table.class}}.
       |     ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘mapsf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) time_plot_event.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_event.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) time_plot_interval.Rd:23: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'rqPen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
'LazyData' is specified without a 'data' directory
Running examples in ‘mthapower-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mthapower
> ### Title: Power calculations - mtDNA haplogroups
> ### Aliases: mthapower
> 
> ### ** Examples
> 
> # Example 1:
> pow <- mthapower(n.cases=203, p0=0.443, Nh=13, OR.cas.ctrl=2.33, sig.level=0.05)
> 
> # Example 2:
> # Create data frames
> pow.H150 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.5, sig.level=0.05)
> pow.H175 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.75, sig.level=0.05)
> pow.H200 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2, sig.level=0.05)
> pow.H250 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2.5, sig.level=0.05)
> 
> # Bind the three data frames:
> bindata <- rbind(pow.H150,pow.H175,pow.H200,pow.H250)
> # Adds column OR to binded data frame:
> bindata$OR <- rep(factor(c(1.50,1.75,2,2.5)),
+               times = c(nrow(pow.H150),
+                         nrow(pow.H175),
+                         nrow(pow.H200),
+                         nrow(pow.H250)))
> # Create plot:
> # install.packages("car")
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘reshape2’

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:
  'magick', 'imager', 'shiny', 'shinydashboard', 'shinyWidgets'

Packages suggested but not available for checking: 'shinytest', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'shiny', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fgsea', 'ggraph', 'plyr', 'Rcpp'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kohonen’
Running examples in ‘mulgar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: som_model
> ### Title: Process the output from SOM to display the map and data
> ### Aliases: som_model
> 
> ### ** Examples
> 
> require(kohonen)
Loading required package: kohonen
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘kohonen’
> data(clusters)
> c_grid <- kohonen::somgrid(xdim = 5, ydim = 5,
+   topo = 'rectangular')
Error in loadNamespace(x) : there is no package called ‘kohonen’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘randomcoloR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘OpenMx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'geometry', 'mirt', 'car', 'dae'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rmumps', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'tram', 'fixest', 'glmmTMB'
Error(s) in re-building vignettes:
  ...
--- re-building ‘chfls1.Rnw’ using Sweave
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data

Attaching package: ‘TH.data’

The following object is masked from ‘package:MASS’:

    geyser

Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
--- finished re-building ‘chfls1.Rnw’

--- re-building ‘generalsiminf.Rnw’ using Sweave
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

The following object is masked from ‘package:MASS’:

    geyser


Attaching package: ‘robustbase’

The following object is masked from ‘package:survival’:

    heart


Error: processing vignette 'generalsiminf.Rnw' failed with diagnostics:
 chunk 2 (label = setup-2) 
Error in library("lme4") : there is no package called ‘lme4’

--- failed re-building ‘generalsiminf.Rnw’

--- re-building ‘multcomp-examples.Rnw’ using Sweave
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

The following object is masked from ‘package:MASS’:

    geyser

Waiting for profiling to be done...
Warning in chkdots(...) :
  Argument(s) ‘abseps’ passed to ‘...’ are ignored
--- finished re-building ‘multcomp-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘generalsiminf.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘pgirmess’
Package required but not available: ‘MTS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MultEq-package.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MultEq-package.Rd:30: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘spelling’
'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.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape2’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘phacking’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ade4', 'car', 'lme4', 'mixlm', 'Rcpp', 'RSpectra', 'RcppEigen'

Packages suggested but not available for checking: 'FactoMineR', 'RGCCA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plotly', 'shiny', 'shinythemes', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'Boruta', 'caret', 'rdist'

Packages suggested but not available for checking: 'switchBox', 'qpdf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) dbivCMP.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{bivprob}{Bivariate probabilities, {p00, p01, p10, p11}.}
       |                                         ^
Packages required but not available: '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: 'lme4', 'pcaMethods'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'pROC', 'lme4', 'lmerTest', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'funData', 'MFPCA', 'sparseFLMM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GFDmcv', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ez', 'reshape2', 'BayesFactor'

Packages suggested but not available for checking: 'plyr', 'ggraph'

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: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'plsgenomics', 'ggrepel', 'qgraph', 'mgm', 'lemon'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'OpenMx', 'hommel'

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:
  'compositions', 'brms', 'shiny', 'shinystan', 'plotly', 'hrbrthemes',
  'DT', 'bayesplot'

Packages suggested but not available for checking: 'lme4', 'cmdstanr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘brms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'spelling', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'lme4', 'lmerTest', 'JWileymisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'klaR', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RecordLinkage', 'Rcpp', 'geosphere', '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: 'prodlim', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'brms', 'glmnetUtils', 'ranger', 'miniLNM', 'phyloseq'

Packages suggested but not available for checking:
  'compositions', 'ggdist', 'ggraph', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'RSpectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'ggraph', 'ggdist', 'bayesplot',
  'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking:
  'splines2', 'flexsurv', 'rstpm2'

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', 'RcppXPtrUtils', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'optmatch', 'matchMulti', 'fields', 'plyr', 'rcbalance', 'rlemon'

Package suggested but not available for checking: ‘rrelaxiv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘interp’

Package suggested but not available for checking: ‘fields’

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: 'meta', 'HardyWeinberg'

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:
  'iBST', 'pec', 'survminer'
Error(s) in re-building vignettes:
  ...
--- re-building ‘test.Rmd’ using rmarkdown

Quitting from lines 72-95 [unnamed-chunk-4] (test.Rmd)
Error: processing vignette 'test.Rmd' failed with diagnostics:
there is no package called 'iBST'
--- failed re-building ‘test.Rmd’

SUMMARY: processing the following file failed:
  ‘test.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) nullestimation.Rd:17: Lost braces; missing escapes or markup?
    17 |           \code{U}        \tab The common latent space vectors. U in R^{n x d}\cr
       |                                                                        ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘qpdf’
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'terra', 'Rcpp', 'raster', 'shiny', 'RcppArmadillo'

Packages suggested but not available for checking: 'tmap', 'magick'

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: ‘sensitivity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lmerTest', 'logistf', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kohonen’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape2'

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: ‘psd’
Packages required but not available: 'flextable', 'ggdist', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘CCA’
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: 'factoextra', 'candisc', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'RSpectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'reshape2', 'glmnet', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'gganimate', 'tidybayes'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ICSNP’

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', 'lme4', 'plyr'

Packages suggested but not available for checking: 'lmerTest', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvnfast', 'bayesplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘MultivariateRandomForest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'gamm4'

Packages which this enhances but not available for checking:
  'aods3', 'caper', 'cplm', 'logistf', 'MCMCglmm', 'spatialreg',
  'splm', 'unmarked', 'glmmTMB', 'maxlike'
Unknown package ‘aods3’ in Rd xrefs
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) metricUnfolding.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:73-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:75-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) metricUnfolding.Rd:80-86: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘flextable’
checkRd: (-1) plotLociHC.Rd:55: Lost braces; missing escapes or markup?
    55 | If \code{value} is one of {0.2,0.4,0.6,0.8,1,2,3,4,5,6,7,8,9,10}
       |                           ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plyr', 'reshape2', 'umap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DescTools', 'pander'
Package suggested but not available for checking: ‘qvalue’
Running examples in ‘mutoss-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Qvalue
> ### Title: Storey's (2001) q-value Procedure...
> ### Aliases: Qvalue
> 
> ### ** Examples
> pval <- c(runif(50), runif(50, 0, 0.01))
> result <- Qvalue(pval)
Loading required package: qvalue
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘qvalue’
Package qvalue is required - should we install it?
Error in requireLibrary("qvalue") : 
  Required package qvalue should not be installed
Calls: Qvalue -> requireLibrary
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘reshape2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_sarted_with_mutSignatures.Rmd’ using rmarkdown

Quitting from lines 15-34 [setup] (get_sarted_with_mutSignatures.Rmd)
Error: processing vignette 'get_sarted_with_mutSignatures.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘get_sarted_with_mutSignatures.Rmd’

SUMMARY: processing the following file failed:
  ‘get_sarted_with_mutSignatures.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘runner’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'pROC', 'caret', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'RLRsim', 'ape', 'sem'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rfast', 'Rfast2'

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: ‘MNM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'penalized', 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'brms', 'marginaleffects', 'Rcpp', 'rstan', 'rstantools',
  'bayesplot', 'mvnfast', 'smooth', 'RcppArmadillo'

Packages suggested but not available for checking:
  'scoringRules', 'cmdstanr', 'splines2', 'extraDistr', 'wrswoR',
  'collapse'

Package which this enhances but not available for checking: ‘gratia’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'geometry', 'CBPS'

Packages suggested but not available for checking: 'dagitty', 'ggdag'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mvmesh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'heplots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mvLSW', 'imputeTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo', 'RcppSpdlog'

Packages suggested but not available for checking: 'GGally', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘meta’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phytools', 'ape', 'spam'

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
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'Rcpp', 'RcppArmadillo', 'RcppDist'

Package suggested but not available for checking: ‘mice’

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: 'plyr', 'energy', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MVNtestchar-package.Rd:16-17: Lost braces; missing escapes or markup?
    16 | {Provides a test of multivariate normality of a sample which does not require estimation of the nuisance parameters, the mean      vector and covariance matrix.  Rather, a sequence of transformations removes these nuisance parameters, resulting in a set of    sample matrices that are positive definite.  If, and only if the original data is multivariate normal, these matrices are       uniformly distributed on the space of positive definite matrices in the unit hyper-rectangle.  The package performs a goodness    of fit test of this hypothesis. In addition to the test, functions in the package give visualizations of the  support region    of positive definite matrices for p equals 2.
       | ^
Package required but not available: ‘minqa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
Packages required but not available: 'libstable4u', 'cubature'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mpoly', 'Rcpp'

Package suggested but not available for checking: ‘spray’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bayesm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'textmineR', 'tidytext', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'PCMBase'

Packages suggested but not available for checking: 'PCMBaseCpp', 'mvMORPH'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cem’

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: ‘cubature’

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: 'nnTensor', 'ccTensor', 'iTensor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'refund', 'reshape2'

Packages suggested but not available for checking:
  'ggpubr', 'refund.shiny', 'Seurat', 'SeuratObject'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘OpenMx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'Rfast', 'energy', 'bigmemory', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fda', 'reticulate', 'caret', 'uwot', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'OpenMx', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rPref', 'shiny'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'plotly'

Package suggested but not available for checking: ‘rTubeDB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'Rcpp', 'RcppSpdlog', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggforce', 'ggrepel', 'shiny', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘survminer’

Packages suggested but not available for checking: 'bestglm', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages which this enhances but not available for checking:
  'MCMCglmm', 'asreml'
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M36NT2PM.dat.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', 'SensoMineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ggraph', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'imputeTS', 'greybox', 'Rfast', 'philentropy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘bib2df’

Package suggested but not available for checking: ‘rcrossref’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘udpipe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘bWGR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'autothresholdr', 'detrendr', 'Rcpp', 'reshape2'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘UpSetR’

Packages suggested but not available for checking:
  'simputation', 'imputeTS', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘later’

Package which this enhances but not available for checking: ‘promises’
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘ccaPP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcppCCTZ', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'spelling'
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Packages suggested but not available for checking: 'spelling', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'ggtext', 'gtsummary', 'quarto', 'rUM'

VignetteBuilder package required for checking but not installed: ‘quarto’
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Package required but not available: ‘rdist’

Packages suggested but not available for checking:
  'ppclust', 'spatialClust'

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 suggested but not available for checking: ‘spelling’
Packages required but not available: 'nat', 'nabor', 'plyr', 'spam'

Packages suggested but not available for checking: 'spelling', 'bigmemory'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'nabor', 'plyr'

Packages suggested but not available for checking:
  'Rvcg', 'alphashape3d', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'plyr'

Packages suggested but not available for checking: 'DT', 'gurobi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nat', 'Morpho'

Packages suggested but not available for checking: 'spelling', 'nabor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinyWidgets', 'raster', 'shinydashboard', 'leaflet',
  'leaflet.extras', 'tidytext', 'fasterize', 'sf', 'tm'

Packages suggested but not available for checking:
  'rnaturalearth', 'lwgeom', 'shinyLP'

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:
  'plotly', 'simts', 'leaflet', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘plyr’
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                 ^
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                         ^
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) nbconvert.Rd:49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) nbconvert.Rd:50: Lost braces in \enumerate; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rrpack', 'glmnet', 'mpath', 'RcppArmadillo'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'poisbinom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'mpath'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RBesT', 'lmerTest', 'spaMM', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘terra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_ncdfCF.Rmd’ using rmarkdown

Quitting from lines 258-276 [cfdata] (Using_ncdfCF.Rmd)
Error: processing vignette 'Using_ncdfCF.Rmd' failed with diagnostics:
there is no package called 'terra'
--- failed re-building ‘Using_ncdfCF.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_ncdfCF.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'sf', 'stars', 'areal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package required but not available: ‘rhoR’

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: 're2', 'reshape2'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'glmnet', 'fields', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ashr’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'energy', 'Rfast', 'leidenAlg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'sf', 'tidycensus'

Packages suggested but not available for checking:
  'DescTools', 'tigris', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘animation’

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: ‘heatmaply’

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:
  'pROC', 'MBESS', 'car', 'ez', 'BayesFactor', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'Rfast', 'Seurat', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DescTools', 'ez', 'WRS2', 'fungible', 'rockchalk', 'MBESS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RDS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinythemes', 'plotly', 'brms', 'rstan', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘terra’
Packages required but not available: 'sf', 'geojsonsf', 'leaflet'

Package suggested but not available for checking: ‘Bchron’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reticulate', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dataone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) color_palette.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:18: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) color_palette.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:29: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet', 'pROC', 'Rfast'

Packages suggested but not available for checking:
  'Boruta', 'fastshap', 'ggpubr', 'hsstan', 'ranger', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'effects'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recipes’

Packages suggested but not available for checking:
  'ggrepel', 'glmnet', 'tune'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘huge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'openxlsx'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggraph', 'reshape2'

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: ‘pcalg’

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', 'MatchIt', 'RcppArmadillo'

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggraph', 'picante', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'reshape2', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘huge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'quickPlot', 'terra'

Packages suggested but not available for checking:
  'fastshp', 'raster', 'sf', 'SpaDES.core', 'SpaDES.tools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggnetwork', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'lme4', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘meta’

Package suggested but not available for checking: ‘cccp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'seqinr'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'poisbinom', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggraph’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'shiny', 'miniUI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘knitcitations’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘bigmemory’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'wTO', 'Rfast', 'cubature'

Package suggested but not available for checking: ‘CoDiNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fable', 'fabletools', 'tsibble'

Package suggested but not available for checking: ‘feasts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘DiagrammeRsvg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shinyBS', 'shiny', 'shinydashboard', 'colourpicker', 'DT', 'ipc',
  'netgwas', 'plotly', 'promises', 'shinycssloaders', 'shinyjs',
  'shinyscreenshot', 'shinyWidgets'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinybusy', 'plotly', 'shinyjs', 'shinyWidgets'

Package suggested but not available for checking: ‘crch’

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: 'mixtools', 'RSpectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) nettskjema_get_data.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_get_data.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_get_data.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_token2renviron.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_token2renviron.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_token2renviron.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_write_codebook.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_write_codebook.Rd:45: Lost braces in \itemize; meant \describe ?
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘GA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) rc.plot.ideogram.Rd:20: Lost braces; missing escapes or markup?
    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
Packages required but not available:
  'qgraph', 'reshape', 'ggrepel', 'GGally', 'ggvis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'reshape2', 'qgraph', 'networktools', 'IsingFit'

Packages suggested but not available for checking:
  'bootnet', 'IsingSampler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'reshape2', 'networktools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘shiny’
Packages required but not available:
  'Rcpp', 'RSpectra', 'graphon', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) harry_potter.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:49: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) nodeLogic.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:36: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) nodeLogic.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:46: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Packages required but not available: 'Rcpp', 'ggrepel'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'randnet', 'RSpectra'

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', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'IsingFit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qgraph', 'reshape2', 'smacof', 'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'reshape2'

Package suggested but not available for checking: ‘fxregime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggpubr’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'tensorflow', 'keras', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking: 'caret', 'RSNNS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'NeuralNetTools', 'reshape2', 'caret', 'ggforce', 'ggrepel'

Packages suggested but not available for checking: 'RSNNS', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'oro.nifti', 'RNifti'

Packages suggested but not available for checking: 'reshape2', 'brainR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggseg’

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: 'oro.nifti', 'fslr'

Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'flipr', 'umap', 'rgeomstats', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ctgt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘devtools’

Packages suggested but not available for checking: 'robotstxt', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyRSS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quanteda', 'quanteda.textstats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

Packages suggested but not available for checking: 'r2resize', 'r2social'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tinysnapshot’
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: 'gt', 'nflplotR'
Packages suggested but not available for checking:
  'DT', 'gsisdecoder', 'qs'
Packages required but not available: 'ggpath', 'gt', 'magick'

Package suggested but not available for checking: ‘webshot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DT', 'qs'
Package suggested but not available for checking: ‘gt’
checkRd: (-1) load_schedules.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
Package required but not available: ‘nflplotR’

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', 'torch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lamW’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'reticulate', 'forecast'

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.
Packages suggested but not available for checking: 'Rtsne', 'umap', 'uwot'

Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Packages suggested but not available for checking: 'odbc', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) NHANES.Rd:278: Lost braces
   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
Packages required but not available:
  'hydroloom', 'sf', 'units', 'maptiles', 'mapsf', 'fst'

Packages suggested but not available for checking:
  'ggmap', 'lwgeom', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'units'

Packages suggested but not available for checking:
  'wikilake', 'crul', 'lwgeom', 's2'

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: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking:
  'caret', 'lme4', 'ModelMetrics', 'ggrepel', 'synthpop'
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'dismo', 'pROC', 'raster', 'spider'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘SIBER’

Packages suggested but not available for checking: 'ggdist', 'ggtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'castor', 'geiger', 'terra'

Package suggested but not available for checking: ‘phytools’

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: ‘oro.nifti’
Running examples in ‘nifti.pbcor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nifti.pbcor_mask
> ### Title: Prepare the mask for a parcel-based correlation between NIfTI
> ###   images
> ### Aliases: nifti.pbcor_mask
> 
> ### ** Examples
> 
> library(oro.nifti)
Error in library(oro.nifti) : there is no package called ‘oro.nifti’
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinyjs', 'shinythemes'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'bipartite', 'mice', 'missMDA', 'tidytext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rcarbon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mcmcse’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘sf’

Packages which this enhances but not available for checking:
  'kokudosuuchi', 'jpndistrict', 'jpmesh'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pander’
Skipping checking math rendering: package 'V8' unavailable
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘car’

Packages suggested but not available for checking:
  'plyr', 'reshape2', 'rsq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'a4Core', 'MLInterfaces', 'ipred'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rfast', 'Rfast2'

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: ‘Rmisc’

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: ‘reshape’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lbfgsb3c', 'minqa', 'n1qn1', 'Rcpp', 'rxode2', 'symengine',
  'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking: 'devtools', 'qs', 'xgxr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggtext', 'nlmixr2est', 'Rcpp', 'rxode2', 'symengine',
  'RcppArmadillo'

Packages suggested but not available for checking: 'brms', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nlmixr2est', 'rxode2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nlmixr2est', 'nlmixr2extra', 'rxode2', 'xgxr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'nlmixr2est', 'nlmixr2extra', 'rxode2', 'nlmixr2plot'

Packages suggested but not available for checking: 'devtools', 'n1qn1'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'flextable', 'ggforce', 'ggpubr', 'nlmixr2', 'nlmixr2extra',
  'onbrand', 'rxode2', 'xpose', 'xpose.nlmixr2'

Package suggested but not available for checking: ‘ggPMX’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Qtools', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Rvmmin', 'Rcgmin'
Skipping checking math rendering: package 'V8' unavailable
Packages which this enhances but not available for checking:
  'udpipe', 'spacyr', 'cleanNLP'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'bde', 'np'

Packages suggested but not available for checking: 'ranger', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘OpenMx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qdap’

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
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'lhs', 'sensitivity', 'raster', 'sf', 'EasyABC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lhs’
checkRd: (-1) anova.Rd:19: Lost braces
    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘Ryacas’
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: 'devtools', 'spelling'
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NlsyLinks)
  > 
  > test_check("NlsyLinks")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 206 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • Save time for now (1): 'test-create-pair-dataset.R:194:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-read-csv.R:1:1'): (code run outside of `test_that()`) ──────────
  <packageNotFoundError/error/condition>
  Error in `library(devtools)`: there is no package called 'devtools'
  Backtrace:
      ▆
   1. └─base::library(devtools) at test-read-csv.R:1:1
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 206 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘about.Rmd’ using rmarkdown
--- finished re-building ‘about.Rmd’

--- re-building ‘collaborators.Rmd’ using rmarkdown
--- finished re-building ‘collaborators.Rmd’

--- re-building ‘facilitating.Rmd’ using rmarkdown
--- finished re-building ‘facilitating.Rmd’

--- re-building ‘faq.Rmd’ using rmarkdown
--- finished re-building ‘faq.Rmd’

--- re-building ‘nls-investigator.Rmd’ using rmarkdown
--- finished re-building ‘nls-investigator.Rmd’

--- re-building ‘nlsy-ace.Rmd’ using rmarkdown

Quitting from lines 469-471 [session-info-2] (nlsy-ace.Rmd)
Error: processing vignette 'nlsy-ace.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘nlsy-ace.Rmd’

--- re-building ‘publications.Rmd’ using rmarkdown
--- finished re-building ‘publications.Rmd’

--- re-building ‘software-and-support.Rmd’ using rmarkdown
--- finished re-building ‘software-and-support.Rmd’

SUMMARY: processing the following file failed:
  ‘nlsy-ace.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) fwtnpperm.Rd:34: Lost braces
    34 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ape’

Packages suggested but not available for checking:
  'TreeSim', 'DDD', 'plyr', 'reshape2', 'TESS', 'DAISIE'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

Packages suggested but not available for checking: 'netmeta', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Packages required but not available: 'netmeta', 'meta', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'meta', 'netmeta'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fst’

Packages suggested but not available for checking: 'NMsim', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'bigmemory', 'synchronicity', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'unmarked'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘openxlsx’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ggpubr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMRphasing_vignette.rmd’ using rmarkdown

Quitting from lines 57-70 [unnamed-chunk-4] (NMRphasing_vignette.rmd)
Error: processing vignette 'NMRphasing_vignette.rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building ‘NMRphasing_vignette.rmd’

SUMMARY: processing the following file failed:
  ‘NMRphasing_vignette.rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NMdata', 'fst'

Packages suggested but not available for checking: 'tracee', 'simpar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'reticulate', 'KernelKnn', 'RcppArmadillo'

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:
  'keras', 'tensorflow', 'reticulate', 'luz', 'torch'

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: 'logistf', 'mice'
Packages required but not available: 'forecast', 'glmnet', 'tsutils'

Package suggested but not available for checking: ‘thief’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘mvnfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'nabor', 'units'

Package suggested but not available for checking: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
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
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pcds’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'tagcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GpGp', 'TruncatedNormal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'choroplethr', 'hurricaneexposure', 'plyr'

Packages suggested but not available for checking:
  'hurricaneexposuredata', 'pander'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘paws’

Package suggested but not available for checking: ‘jsonify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘V8’

Packages suggested but not available for checking: 'sofa', 'elastic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘word2vec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ape', 'phangorn', 'DDD', 'phylobase', 'geiger', 'beautier',
  'beastier', 'tracerer'

Packages suggested but not available for checking:
  'TreeSim', 'nLTT', 'RPANDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'picante', 'raster', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) simulatePop.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:45: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'caret', 'RSNNS', 'C50'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘philentropy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SILGGM', 'huge', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fracture’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rsdmx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘webshot2’

Packages suggested but not available for checking:
  'V8', 'shinytest', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘do’

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', 'glmnet', 'pROC'

Package suggested but not available for checking: ‘ClusterR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CondIndTests’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'tsDyn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'latticeExtra', 'splines2', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'rxode2', 'qs', 'ggforce'

Packages suggested but not available for checking:
  'devtools', 'NMdata', 'nonmem2R', 'xgxr', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pander’
Error(s) in re-building vignettes:
  ...
--- re-building ‘parameter-table.Rmd’ using rmarkdown

Quitting from lines 193-195 [unnamed-chunk-20] (parameter-table.Rmd)
Error: processing vignette 'parameter-table.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘parameter-table.Rmd’

SUMMARY: processing the following file failed:
  ‘parameter-table.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 suggested but not available for checking:
  'mirt', 'OpenMx', 'tidySEM', 'AER', 'faraway'
Package required but not available: ‘cubature’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'caret', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'np', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MCMCglmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) set.data.Rd:14: Lost braces; missing escapes or markup?
    14 |   \item{shape}{either \code{wide} or {long}. Default \code{wide}. See Details.}
       |                                      ^
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DT', 'shiny', 'shinyalert', 'shinyBS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘HadamardR’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) mle_parameters.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'car', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'plotly', 'hexSticker'

Package suggested but not available for checking: ‘learnr’

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: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

Packages suggested but not available for checking:
  'ggnetwork', 'gganimate', 'ape', 'tidytree', 'treeio', 'ggtree'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bipartite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘brms’
Package required but not available: ‘ggpattern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘NoviceDeveloperResources’

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.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'reshape2', 'bayesplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DT', 'mmints', 'npboottprm', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DT', 'MKinfer', 'mmints', 'shiny', 'shinythemes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Benchmarking', 'np'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GDINA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'smotefamily', 'caret'

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.
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', 'reshape2', 'GGally', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) DiscHazRateAuxFunctions.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:48: Lost braces in \itemize; meant \describe ?
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:
  'shiny', 'shinycssloaders'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘survminer’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ez', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) nplr.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:52-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:56-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:82: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Packages required but not available: 'terra', 'ks'

Packages suggested but not available for checking: 'leaflet', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘cubature’

Package suggested but not available for checking: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SPEI’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Packages suggested but not available for checking: 'profileR', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spam’

Packages suggested but not available for checking: 'gstat', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) np.reg.test.Rd:148: Lost braces
   148 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
checkRd: (-1) nptest-package.Rd:73: Lost braces
    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'srvyr', 'survey', 'svrep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘StepwiseTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) NSAE.Rd:14: Lost braces; missing escapes or markup?
    14 | {Maintainer}: Saurav Guha \email{saurav.iasri@gmail.com}
       | ^
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'CCA', 'glmnet', 'V8'
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) NScluster-package.Rd:30-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:35-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:44-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:49-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:44-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:69-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:113-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:36-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:90-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:123-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:151-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:195-211: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'mcmcse', 'np'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rPref’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘NSM3’
Package required but not available: ‘np’

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: ‘sde’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'BIEN', 'vcr'
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NSR)
  > 
  > 
  > test_check("NSR")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/NSR.Rcheck/tests/testthat/setup-nsr.R"
  Caused by error in `library()`:
  ! there is no package called 'vcr'
  Backtrace:
       ▆
    1. ├─testthat::test_check("NSR")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("vcr") at tests/testthat/setup-nsr.R:12:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Packages required but not available: 'ape', 'bigmemory', 'iCAMP'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cartographer', 'sf'

Package suggested but not available for checking: ‘nngeo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) MSM.fit.Rd:21: Lost braces
    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
checkRd: (-1) SMC.Smooth.Rd:25: Lost braces; missing escapes or markup?
    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
checkRd: (-1) SMC.Smooth.Rd:26: Lost braces; missing escapes or markup?
    26 | {logww} (their corresponding log weight).}
       | ^
Package required but not available: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘forecast’
Running examples in ‘nullabor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: null_ts
> ### Title: Generate null data by simulating from a time series model.
> ### Aliases: null_ts
> 
> ### ** Examples
> 
> require(forecast)
Loading required package: forecast
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘forecast’
> require(ggplot2)
Loading required package: ggplot2
> require(dplyr)
Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> data(aud)
> l <- lineup(null_ts("rate", auto.arima), aud)
Error: object 'auto.arima' not found
Execution halted
Packages required but not available:
  'ape', 'ggraph', 'ggtree', 'hahmmr', 'parallelDist', 'pryr', 'Rcpp',
  'scistreer', 'vcfR', 'RcppArmadillo', 'roptim'

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'text2vec'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘huge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'eurostat', 'ggfittext', 'ggpubr', 'ggrepel', 'raster', 'sf', 'terra'
Package suggested but not available for checking: ‘nonlinearTseries’
Running examples in ‘NVAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NVAR
> ### Title: Fit a nonlinear vector autoregression model
> ### Aliases: NVAR
> 
> ### ** Examples
> 
> # generate test data from the Lorenz system
> testdata <- nonlinearTseries::lorenz()
Error in loadNamespace(x) : there is no package called ‘nonlinearTseries’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'dae', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'geosphere', 'spelling'
checkRd: (-1) xyz2R.Rd:31: Lost braces
    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘position-calculations.Rmd’ using rmarkdown

Quitting from lines 359-360 [example-05-geodesic] (position-calculations.Rmd)
Error: processing vignette 'position-calculations.Rmd' failed with diagnostics:
there is no package called 'geosphere'
--- failed re-building ‘position-calculations.Rmd’

SUMMARY: processing the following file failed:
  ‘position-calculations.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘GGally’
Error(s) in re-building vignettes:
  ...
--- re-building ‘README.Rmd’ using rmarkdown

Quitting from lines 64-82 [unnamed-chunk-3] (README.Rmd)
Error: processing vignette 'README.Rmd' failed with diagnostics:
there is no package called 'GGally'
--- failed re-building ‘README.Rmd’

SUMMARY: processing the following file failed:
  ‘README.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'Rcpp', 'geosphere', 'outbreaker2'

Packages suggested but not available for checking:
  'tigris', 'sf', 'socialmixr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ggrepel', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cubature’

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.
Packages required but not available: 'shiny', 'miniUI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'pec', 'glmnet', 'prodlim', 'RcppArmadillo'

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.
checkRd: (-1) OBMb.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ape', 'bib2df', 'BIEN', 'rgbif', 'RefManageR', 'leaflet', 'waffle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'text2vec', 'tm'

Packages suggested but not available for checking:
  'plumber', 'devtools', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
Packages required but not available:
  'stars', 'shiny', 'sf', 'waiter', 'shinyFeedback', 'miniUI', 'DT',
  'shinyjs'

Packages suggested but not available for checking: 'shinytest', 'spelling'

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:
  'shiny', 'shinyBS', 'sf', 'shinyjs', 'shinythemes', 'DT', 'leaflet',
  'leaflet.extras', 'lwgeom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'reshape2', 'fields', 'ggedit', 'sf', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘oce’
Error(s) in re-building vignettes:
  ...
--- re-building ‘oceanwaves-vignette.Rmd’ using rmarkdown

Quitting from lines 76-77 [loadoce] (oceanwaves-vignette.Rmd)
Error: processing vignette 'oceanwaves-vignette.Rmd' failed with diagnostics:
there is no package called 'oce'
--- failed re-building ‘oceanwaves-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘oceanwaves-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'automap', 'interp', 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'orf', 'glmnet', 'ranger', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixture', 'dbscan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'spam', 'Rcpp', 'adespatial', 'spdep', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
checkRd: (-1) ocsApiUserProvisioningManager.Rd:87: Lost braces
    87 |  \item{code{addToGroup(userid, groupid)}}{
       |            ^
Packages required but not available: 'DT', 'shiny', 'shinyAce', 'shinyjs'

Package suggested but not available for checking: ‘odbc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fable', 'fabletools', 'lookout', 'tsibble'

Packages suggested but not available for checking: 'DDoutlier', 'feasts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggrepel', 'gt', 'qs', 'Rcpp'
Packages required but not available: 'caret', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'RcppRoll', 'reshape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘morse’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sensitivity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ppclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘jsonvalidate’
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geosphere', 'ggmap', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sfheaders’

Packages suggested but not available for checking: 'lwgeom', 'nngeo', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘spelling’

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: 'magick', 'DiagrammeRsvg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readsdmx’

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: 'hexSticker', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigmemory', 'Rcpp', 'RcppEigen', 'RSpectra', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'openxlsx', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘estimatr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rvg’

Packages suggested but not available for checking: 'flextable', 'doconv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'doconv', 'magick'
Running ‘testthat.R’ [40s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(officer)
  +   library(xml2)
  + })
  > 
  > test_check("officer")
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 910 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-missing-tableStyles.R:2:3'
  • doconv cannot be loaded (6): 'test-pptx-add.R:9:3', 'test-pptx-add.R:25:3',
    'test-pptx-add.R:53:3', 'test-pptx-add.R:72:3', 'test-pptx-add.R:97:3',
    'test-pptx-info.R:81:3'
  • empty test (1): 'test-pptx-add.R:511:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-to_rtf.R:23:3'): to_rtf works with fpar and external images ────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'magick'
  Backtrace:
       ▆
    1. ├─testthat::expect_true(grepl("Hello World, ", to_rtf(fpar_1))) at test-to_rtf.R:23:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::grepl("Hello World, ", to_rtf(fpar_1))
    5. │ └─base::is.factor(x)
    6. ├─officer::to_rtf(fpar_1)
    7. ├─officer:::to_rtf.fpar(fpar_1)
    8. │ └─base::lapply(chks, to_rtf)
    9. │   ├─officer (local) FUN(X[[i]], ...)
   10. │   └─officer:::to_rtf.external_img(X[[i]], ...)
   11. └─base::loadNamespace(x)
   12.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   13.     └─base (local) withOneRestart(expr, restarts[[1L]])
   14.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 910 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'glmnet', 'recipes', 'tune'
Running examples in ‘offsetreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glmnet_offset
> ### Title: Fit Penalized Generalized Linear Models with an Offset
> ### Aliases: glmnet_offset
> 
> ### ** Examples
> 
> us_deaths$off <- log(us_deaths$population)
> x <- model.matrix(~ age_group + gender + off, us_deaths)[, -1]
> glmnet_offset(x, us_deaths$deaths, family = "poisson", offset_col = "off")
Error in glmnet_offset(x, us_deaths$deaths, family = "poisson", offset_col = "off") : 
  The package "glmnet" is required.
Calls: glmnet_offset -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage.Rmd’ using rmarkdown

Quitting from lines 28-42 [glm] (usage.Rmd)
Error: processing vignette 'usage.Rmd' failed with diagnostics:
there is no package called 'recipes'
--- failed re-building ‘usage.Rmd’

SUMMARY: processing the following file failed:
  ‘usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'sf', 'lwgeom', 'ggpubr', 'ggExtra', 'terra', 'tmap', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ade4’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                            ^
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                                                         ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'tigger', 'alakazam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cvms', 'ggmcmc'

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: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonsf', 'sf'

Packages suggested but not available for checking:
  'mapview', 'nominatimlite', 'osmdata', 'spelling', 'tmaptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'warbleR', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rapportools', 'Deducer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘urltools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘websocket’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'ggpubr', 'ggrepel', 'rstatix'

Packages suggested but not available for checking:
  'clusterProfiler', 'FSA', 'lme4', 'lmerTest', 'umap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'xplorerr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'golem', 'shiny', 'shinybusy', 'shinythemes', 'summarytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'opencpu', 'plotly', 'UpSetR'
Error(s) in re-building vignettes:
  ...
--- re-building ‘OmicNavigatorAPI.Rnw’ using Sweave
OmicNavigator R package version: 1.13.13
The app is not installed. Install it with installApp()
Installing study "ABC" in /home/hornik/tmp/scratch/RtmplzdQIf/file1c14b680c0579
Exporting study "ABC" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown <unknown@unknown>
Calculating pairwise overlaps. This may take a while...
Exported study to /home/hornik/tmp/scratch/RtmplzdQIf/ONstudyABC

Error: processing vignette 'OmicNavigatorAPI.Rnw' failed with diagnostics:
 chunk 3 (label = test-data) 
Error in utils::install.packages(tmpPkgDir, lib = library, repos = NULL,  : 
  (converted from warning) installation of package ‘/home/hornik/tmp/scratch/RtmplzdQIf/ONstudyABC’ had non-zero exit status

--- failed re-building ‘OmicNavigatorAPI.Rnw’

--- re-building ‘OmicNavigatorUsersGuide.Rnw’ using Sweave
OmicNavigator R package version: 1.13.13
The app is not installed. Install it with installApp()
Installing study "vignetteExample" in /home/hornik/tmp/scratch/Rtmpp95VuH/file1c176b18495024
Exporting study "vignetteExample" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown <unknown@unknown>
Calculating pairwise overlaps. This may take a while...
Exported study to /home/hornik/tmp/scratch/Rtmpp95VuH/ONstudyvignetteExample
Success!
Returning "default" features for modelID "modelThatDoesntExistYet"
--- finished re-building ‘OmicNavigatorUsersGuide.Rnw’

SUMMARY: processing the following file failed:
  ‘OmicNavigatorAPI.Rnw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘BoutrosLab.plotting.general’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bs4Dash', 'DT', 'golem', 'shiny'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'flextable', 'gt', 'odbc'
Running examples in ‘OmopSketch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tableOmopSnapshot
> ### Title: Create a visual table from a summarise_omop_snapshot result.
> ### Aliases: tableOmopSnapshot
> 
> ### ** Examples
> 
> cdm <- mockOmopSketch(numberIndividuals = 10)
> 
> result <- summariseOmopSnapshot(cdm)
> 
> result |>
+   tableOmopSnapshot()
! Results have not been suppressed.
Error in loadNamespace(x) : there is no package called ‘gt’
Calls: tableOmopSnapshot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'DT', 'shiny'

Packages suggested but not available for checking:
  'gt', 'plotly', 'shinycssloaders', 'shinyWidgets', 'sortable',
  'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'FSA', 'rstatix', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RoeDeerMass-simulation.Rnw’ using Sweave

Error: processing vignette 'RoeDeerMass-simulation.Rnw' failed with diagnostics:
 chunk 6 (label = testTF) 
Error in loadNamespace(x) : there is no package called ‘lme4’

--- failed re-building ‘RoeDeerMass-simulation.Rnw’

SUMMARY: processing the following file failed:
  ‘RoeDeerMass-simulation.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flextable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘anytime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'bayesplot', 'RcppEigen',
  'StanHeaders'

Package suggested but not available for checking: ‘cmdstanr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survminer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppNumerical', 'rstan', 'rstantools', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'glmnet', 'TCGAbiolinks'

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.
checkRd: (-1) oncotree.fit.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'pROC', 'caret'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'ckanr', 'openxlsx'

Packages suggested but not available for checking:
  'DT', 'shinythemes', 'shinyWidgets', 'bs4Dash', 'shinyjs',
  'listviewer'

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: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'plotly', 'reshape2', 'Rcpp', 'smacof', 'princurve', 'ggpubr', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘survminer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ivreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘extraDistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
checkRd: (-1) one_sample.Rd:40: Lost braces; missing escapes or markup?
    40 | In two sided or one sided interval estimation of \code{sigma^2} of one normal sample, {side} is a parameter used to control whether to compute two sided or one sided interval estimation. When computing the one sided upper limit, input \code{side = -1}; when computing the one sided lower limit, input \code{side = 1}; when computing the two sided limits, input \code{side = 0} (default).
       |                                                                                       ^
Package required but not available: ‘car’

Package suggested but not available for checking: ‘AID’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘freealg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘VIM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSpectra', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'shiny', 'shinydashboard', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fuzzyjoin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seededlda', 'shiny', 'quanteda'

Packages suggested but not available for checking:
  'keyATM', 'text2vec', 'BTM', 'topicmodels', 'stm',
  'quanteda.textmodels', 'shinytest2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available:
  'caret', 'forecast', 'glmnet', 'imputeTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Error(s) in re-building vignettes:
  ...
--- re-building ‘oosseVignette.Rmd’ using rmarkdown

Quitting from lines 152-166 [predRf] (oosseVignette.Rmd)
Error: processing vignette 'oosseVignette.Rmd' failed with diagnostics:
object 'onWindows' not found
--- failed re-building ‘oosseVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘oosseVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ggspatial', 'ggtext', 'leaflet', 'openair', 'prettymapr', 'sf'

Packages suggested but not available for checking: 'shiny', 'worldmet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'latticeExtra', 'Rcpp'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘crul’

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
License stub is invalid DCF.
GNU make is a SystemRequirements.
Packages required but not available: 'httpuv', 'protolite'

Package suggested but not available for checking: ‘pander’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'secr', 'plyr', 'Rcpp'

Package suggested but not available for checking: ‘secrlinear’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'ckanr', 'sf'

Package suggested but not available for checking: ‘ggiraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘sf’

Packages suggested but not available for checking: 'stars', 'DT', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'seqinr', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'shiny', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidytext’
Running examples in ‘openintro-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ipo
> ### Title: Facebook, Google, and LinkedIn IPO filings
> ### Aliases: ipo
> ### Keywords: corpus datasets ipo mining text
> 
> ### ** Examples
> 
> 
> library(tidytext)
Error in library(tidytext) : there is no package called ‘tidytext’
Execution halted
Package required but not available: ‘raster’

Package suggested but not available for checking: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'plumber', 'shiny'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'MSEtool', 'DLMtool', 'SAMtool'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'RcppEigen', 'StanHeaders', 'rpf'

Packages suggested but not available for checking:
  'rpf', 'lme4', 'umx', 'ifaTools', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘openNLPmodels.en’
Packages required but not available:
  'shiny', 'shinyjs', 'shinyBS', 'shinythemes', 'shinyWidgets',
  'shinydashboard', 'shinydashboardPlus', 'shinycssloaders',
  'shinyFeedback', 'rintrojs', 'openxlsx', 'DT', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geojsonsf', 'jsonvalidate', 'leaflet', 'V8'

Packages suggested but not available for checking:
  'googlePolylines', 'lwgeom', 'mapview', 'sf', 'units'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggmap', 'magick', 'dbscan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'hyperSpec', 'mmand', 'plotly', 'glmnet', 'shiny'

Packages suggested but not available for checking:
  'shinyjs', 'shinyWidgets', 'bs4Dash', 'DT'

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:
  'googlePolylines', 'RcppSimdJson', 'sf', 'sfheaders'

Package suggested but not available for checking: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘nbc4va’
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘rvg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen'

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AdaptGauss', 'DataVisualizations', 'DistributionOptimization',
  'mixtools', 'mixAK', 'multimode', 'ClusterR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidytext', 'likert', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MonteCarlo.Rd:23: Lost braces
    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ape', 'tidytree', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'gurobi', 'ggtree', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘LambertW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Package required but not available: ‘ipred’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Ckmeans.1d.dp', 'Rcpp', 'reshape2'

Package suggested but not available for checking: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Packages suggested but not available for checking:
  'DT', 'shinydashboard', 'shinyalert', 'plotly', 'hrbrthemes',
  'shinyjs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) drawdesign.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:44: Lost braces in \itemize; meant \describe ?
Package required but not available: ‘did’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dbscan', 'ggrepel', 'plyr', 'reshape2'
Running examples in ‘opticskxi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fortify_ica
> ### Title: Get and fortify ICA
> ### Aliases: fortify_ica
> 
> ### ** Examples
> 
> df_ica <- fortify_ica(iris[-5], n.comp = 2)
Error in loadNamespace(x) : there is no package called ‘plyr’
Calls: fortify_ica ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘opticskxi.Rnw’ using Sweave

Error: processing vignette 'opticskxi.Rnw' failed with diagnostics:
 chunk 2 (label = shape_ds3) 
Error in loadNamespace(x) : there is no package called 'dbscan'

--- failed re-building 'opticskxi.Rnw'

SUMMARY: processing the following file failed:
  'opticskxi.Rnw'

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) gnu_style.Rd:24: Lost braces
    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plyr’

Package which this enhances but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) calc_n_from_c.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Helper function to calculate other n's given n_{1,T} and allocation ratios}
       |                                                       ^
checkRd: (-1) calc_n_from_c.Rd:15: Lost braces; missing escapes or markup?
    15 | Helper function to calculate other n's given n_{1,T} and allocation ratios
       |                                                ^
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'DT', 'shiny', 'shinytest', 'survey'
Running ‘testthat.R’ [43s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optimall)
  > 
  > test_check("optimall")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 246 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-optimall_shiny.R:4:1'): (code run outside of `test_that()`) ────
  <packageNotFoundError/error/condition>
  Error in `library(shinytest)`: there is no package called 'shinytest'
  Backtrace:
      ▆
   1. └─base::library(shinytest) at test-optimall_shiny.R:4:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 246 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘GreedyExperimentalDesign’

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: 'DepthProc', 'fields', 'spam'

Package suggested but not available for checking: ‘lhs’

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.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lbfgsb3c', 'oeli', 'TestFunctions'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spam', 'lbfgsb3c'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'cubature'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mvabund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'minqa', 'lbfgsb3c', 'lbfgs'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'plyr', 'pedigree', 'reshape2', 'optiSolve', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'cccp', 'smacof'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cccp', 'plyr', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'shiny', 'shinydashboard'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'rlemon'

Packages suggested but not available for checking:
  'survey', 'arm', 'pander', 'rrelaxiv'

Package which this enhances but not available for checking: ‘CBPS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘labdsv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Package required but not available: ‘ranger’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSpectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘osqp’

Package suggested but not available for checking: ‘twang’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'reshape2', 'openxlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'embed', 'recipes', 'rstanarm', 'themis'
Packages required but not available: 'latticeExtra', 'Rcpp', 'sf', 'terra'

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'brms', 'transformr', 'gganimate'

Packages suggested but not available for checking:
  'gt', 'marginaleffects', 'collapse', 'glmmTMB', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gRbase’

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
'LazyData' is specified without a 'data' directory
checkRd: (-1) internal.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:70: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'DESeq2', 'devtools', 'dclone'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'verification'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'glmnet', 'penalized'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘lme4’
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) minK.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:15: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘RLRsim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

Packages suggested but not available for checking: 'mlpack', 'heplots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'glmnet', 'forecast'
Error(s) in re-building vignettes:
  ...
--- re-building ‘generalizedCV.Rmd’ using rmarkdown

Quitting from lines 282-317 [unnamed-chunk-3] (generalizedCV.Rmd)
Error: processing vignette 'generalizedCV.Rmd' failed with diagnostics:
there is no package called 'forecast'
--- failed re-building ‘generalizedCV.Rmd’

SUMMARY: processing the following file failed:
  ‘generalizedCV.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) distsumlpmin.Rd:69: Lost braces
    69 |   \code{Véase}{Vease} \enc{también}{tambien} \code{\link{distsummin}}, \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |               ^
checkRd: (-1) distsummin.Rd:80: Lost braces
    80 | \code{Véase}{Vease} \enc{también}{tambien} \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |             ^
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘pander’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ormPlot.Rmd’ using rmarkdown

Quitting from lines 47-49 [unnamed-chunk-3] (ormPlot.Rmd)
Error: processing vignette 'ormPlot.Rmd' failed with diagnostics:
there is no package called 'pander'
--- failed re-building ‘ormPlot.Rmd’

SUMMARY: processing the following file failed:
  ‘ormPlot.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘oro.nifti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RNifti’

Packages which this enhances but not available for checking:
  'fmri', 'oro.dicom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'oro.dicom', 'oro.nifti'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'bio3d', 'castor', 'phangorn', 'phytools', 'seqinr',
  'TreeTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) polynomial.derivatives.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:21: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tm', 'tidytext', 'topicmodels'

Packages suggested but not available for checking: 'reshape2', 'qpdf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

Packages suggested but not available for checking: 'ePCR', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘raster’

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: ‘geojsonsf’

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'lhs', 'twinning', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘crul’

Packages suggested but not available for checking: 'spelling', 'vcr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Luminescence', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'httpuv', 'sf'
Running examples in ‘osmapiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: set_osmapi_connection
> ### Title: Configure connections from osmapiR
> ### Aliases: set_osmapi_connection get_osmapi_url set_osmapi_url
> 
> ### ** Examples
> 
> ori <- get_osmapi_url()
> set_osmapi_connection(server = "testing")
Error in normalize_redirect_uri(redirect_uri = redirect_uri, host_name = host_name,  : 
  The package "httpuv" is required desktop OAuth
Calls: set_osmapi_connection ... <Anonymous> -> normalize_redirect_uri -> check_installed
Execution halted
Package required but not available: ‘collapse’

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', 'sf'

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: 'OpenStreetMap', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RcppSimdJson', 'mapiso', 'googlePolylines', 'sf'

Package suggested but not available for checking: ‘mapsf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘netmeta’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Quitting from lines 120-124 [unnamed-chunk-11] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'netmeta'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘hypervolume’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'pec', 'prodlim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ghql', 'ggiraphExtra', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'umap', 'HDclust', 'dbscan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘transport’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonsf', 'sf', 'urltools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mice', 'missMDA', 'plyr', 'FactoMineR', 'StatMatch', 'rdist'

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: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ape’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'ape'

Package suggested but not available for checking: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ape’
Package suggested but not available for checking: ‘spelling’
checkRd: (-1) fmat.Rd:15: Lost braces; missing escapes or markup?
    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
checkRd: (-1) fmat.Rd:24: Lost braces; missing escapes or markup?
    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
checkRd: (-1) fmat.Rd:25: Lost braces; missing escapes or markup?
    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
checkRd: (-1) fmat.Rd:26: Lost braces; missing escapes or markup?
    26 | produce {eUH, eUO}.
       |         ^
checkRd: (-1) middleearth.Rd:14: Lost braces; missing escapes or markup?
    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
Packages required but not available: 'ranger', 'missRanger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'airt', 'apcluster'

Package suggested but not available for checking: ‘DDoutlier’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'HDoutliers', 'FastPCS', 'cellWise', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'forecast', 'SLBDD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ranger', 'missRanger', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'geiger', 'phytools', 'paleotree', 'phangorn', 'lhs',
  'interp', 'phylolm'

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: ‘sf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Readshapefiles.Rnw’ using Sweave
Loading required package: spatstat.data
Loading required package: spatstat.univar
spatstat.univar 3.0-1
spatstat.geom 3.3-3

Error: processing vignette 'Readshapefiles.Rnw' failed with diagnostics:
 chunk 3 
Error in library(sf) : there is no package called 'sf'

--- failed re-building 'Readshapefiles.Rnw'

SUMMARY: processing the following file failed:
  'Readshapefiles.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘suntools’

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: ‘bigmemory’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sf’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

Packages suggested but not available for checking: 'devtools', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'twang', 'Amelia', 'devtools', 'ggrepel', 'metR', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppEigen', 'RcppNumerical'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'sf', 'spdep'

Packages suggested but not available for checking:
  'concaveman', 'units', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'pander', 'shiny', 'shinyjs', 'shinybusy'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘available’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'devtools', 'rasciidoc', 'spelling'

VignetteBuilder package required for checking but not installed: ‘rasciidoc’
checkRd: (-1) lint_package.Rd:20: Lost braces
    20 | code{\link[lintr:lint_package]{lintr::lint_package}} where we hardcode the
       |     ^
checkRd: (-1) provide_news_rd.Rd:22: Lost braces
    22 | Christian Vonderach uses the index thus wants file{inst/NEWS.rd} to
       |                                                   ^
checkRd: (-1) provide_news_rd.Rd:23: Lost braces
    23 | automatically be in sync with file{./NEWS.md}.
       |                                   ^
Running examples in ‘packager-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create
> ### Title: Create a Package Template
> ### Aliases: create
> 
> ### ** Examples
> 
> path <- file.path(tempdir(), "myFirstPackage")
> packager::create(path = path, fakemake = "roxygen2")
* Adding `.Rprofile` to /home/hornik/tmp/scratch/Rtmphd0q1S/myFirstPackage/.gitignore
* Adding `*.tar.gz` to /home/hornik/tmp/scratch/Rtmphd0q1S/myFirstPackage/.gitignore
* Adding `myFirstPackage.Rcheck` to /home/hornik/tmp/scratch/Rtmphd0q1S/myFirstPackage/.gitignore
* Creating `Makefile` from template.
* Adding `Makefile` to `.Rbuildignore`.
Warning in update_description(path = path, title = tools::toTitleCase(title),  :
  Argument 'author_at_r' is missing, using default.
Warning in read.dcf(path) :
  cannot open compressed file '', probable reason 'No such file or directory'
Error in read.dcf(path) : cannot open the connection
Calls: <Anonymous> ... suggests_dep -> read_dcf -> colnames -> is.data.frame -> read.dcf
Execution halted
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: ‘ggiraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘golem’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ade4', 'pROC', 'FactoMineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘penalized’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'Rtsne', 'ggrepel'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rcpp', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggpubr’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_pafr.Rmd’ using rmarkdown

Quitting from lines 83-91 [alen] (Introduction_to_pafr.Rmd)
Error: processing vignette 'Introduction_to_pafr.Rmd' failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building ‘Introduction_to_pafr.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_to_pafr.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'later', 'servr', 'httpuv', 'websocket'

Packages suggested but not available for checking:
  'promises', 'xaringan', 'pdftools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'devtools'
Running examples in ‘pagemap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pagemap-shiny
> ### Title: Shiny bindings for pagemap
> ### Aliases: pagemap-shiny pagemapOutput renderPagemap
> 
> ### ** Examples
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
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:
  'N2R', 'plyr', 'Rcpp', 'Rtsne', 'sccore', 'urltools',
  'RcppArmadillo', 'RcppEigen'

Packages suggested but not available for checking:
  'dbscan', 'pcaMethods', 'scde', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘alr4’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘MCPAN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Ch.Rd:297: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:214: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:215: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:109: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:110: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:336: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:337: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:88: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:89: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:308: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:309: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:362: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:363: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:70: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:243: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:244: Lost braces in \enumerate; meant \describe ?
Package required but not available: ‘ggrepel’

Packages suggested but not available for checking:
  'units', 'gstat', 'sf', 'analogue'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'sf', 'geosphere', 'h3jsr'

Packages suggested but not available for checking: 'paleotree', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking:
  'pROC', 'ashr', 'CorShrink'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘terra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ape’
Running examples in ‘paleobuddy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find.lineages
> ### Title: Separate a paleobuddy simulation into monophyletic clades
> ### Aliases: find.lineages
> 
> ### ** Examples
> 
> ###
> # first, we run a simple simulation with one starting species
> 
> # set seed
> set.seed(1)
> 
> # run simulation with a minimum of 20 species
> sim <- bd.sim(n0 = 3, lambda = 0.1, mu = 0.1, tMax = 10, 
+               nFinal = c(20, Inf))
> 
> # get a simulation object with the clade originating from species 2
> clades <- find.lineages(sim, S = 2)
> 
> # now we can check to make sure the subclade was correctly separated
> 
> # change NA to 0 on the clade's TE
> clades[[1]]$sim$TE[clades[[1]]$sim$EXTANT] <- 0
> 
> # plot the phylogeny
> if (requireNamespace("ape", quietly = TRUE)) {
+   plot <- ape::plot.phylo(
+     make.phylo(clades[[1]]$sim),
+     main = "red: extinction events \n blue: speciation events");
+   ape::axisPhylo()
+ }
> 
> # check speciation times
> for (j in 2:length(clades[[1]]$sim$TS)) {
+   # the subtraction is just to adjust the wt with the plot scale
+   lines(x = c(
+     sort(clades[[1]]$sim$TS, decreasing = TRUE)[2] -
+        clades[[1]]$sim$TS[j],
+     sort(clades[[1]]$sim$TS, decreasing = TRUE)[2] -
+        clades[[1]]$sim$TS[j]),
+     y = c(plot$y.lim[1], plot$y.lim[2]), lwd = 2, col = "blue")
+ }
Error in plot$y.lim : object of type 'closure' is not subsettable
Calls: lines -> lines.default -> plot.xy -> xy.coords
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/paleobuddy.Rcheck/vign_test/paleobuddy/vignettes/overview_files/figure-gfm/unnamed-chunk-3-1.png
2100x1500 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 38405 bytes
Input file size = 39311 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 33574
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 33273
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 33273

Output IDAT size = 33273 bytes (5132 bytes decrease)
Output file size = 33351 bytes (5960 bytes = 15.16% decrease)


Quitting from lines 76-86 [unnamed-chunk-4] (overview.Rmd)
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'ape'
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ape’

Packages suggested but not available for checking: 'strap', 'divDyn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'poems', 'sf', 'trend'

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phangorn', 'phytools'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking: 'gt', 'sf'
Package suggested but not available for checking: ‘recipes’
Packages required but not available: 'Rcpp', 'minqa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'raster', 'stars'
Packages suggested but not available for checking:
  'latticeExtra', 'reshape2'
Packages required but not available: 'readmoRe', 'plyr', 'robustHD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcppRoll', 'rerddap', 'geosphere'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmerTest', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'PAMmisc', 'reticulate', 'geosphere', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'geosphere', 'sf', 'PAMmisc', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking:
  'reshape', 'Epi', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openxlsx’

Package suggested but not available for checking: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'CBPS', 'RcppArmadillo', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'jtools', 'lmerTest'

Packages suggested but not available for checking: 'brms', 'car', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fixest’

Package suggested but not available for checking: ‘gt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plm', 'matlib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape2’

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: 'crul', 'oai'

Package suggested but not available for checking: ‘vcr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) hvidovre.Rd:11: Lost braces
    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
checkRd: (-1) hvidovre.Rd:25: Lost braces
    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
checkRd: (-1) hvidovre.Rd:26: Lost braces
    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
Package suggested but not available for checking: ‘lme4’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘magick’
Error(s) in re-building vignettes:
  ...
--- re-building ‘PS1_Cat.Rmd’ using rmarkdown
--- finished re-building ‘PS1_Cat.Rmd’

--- re-building ‘PS1_Images.Rmd’ using rmarkdown

Quitting from lines 19-21 [setup] (PS1_Images.Rmd)
Error: processing vignette 'PS1_Images.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building ‘PS1_Images.Rmd’

SUMMARY: processing the following file failed:
  ‘PS1_Images.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'afex', 'BayesFactor', 'car', 'ggforce', 'lme4', 'lmerTest', 'MBESS',
  'spelling'
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("papaja")
  Loading required package: tinylabels
  > 
  > test_check("papaja")
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/papaja.Rcheck/tests/testthat/helper-structure.R"
  Caused by error in `packageVersion()`:
  ! there is no package called 'afex'
  Backtrace:
       ▆
    1. ├─testthat::test_check("papaja")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─utils::packageVersion("afex") at tests/testthat/helper-structure.R:4:1
   15. │                         └─base::stop(packageNotFoundError(pkg, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'shinythemes', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package which this enhances but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lhs', 'spacefillr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘indepth.Rmd’ using rmarkdown

Quitting from lines 296-299 [unnamed-chunk-19] (indepth.Rmd)
Error: processing vignette 'indepth.Rmd' failed with diagnostics:
The following packages could not be loaded: lhs
--- failed re-building ‘indepth.Rmd’

SUMMARY: processing the following file failed:
  ‘indepth.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'compositions', 'ggpubr'

Packages suggested but not available for checking:
  'MicrobiotaProcess', 'phyloseq', 'TreeSummarizedExperiment'

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:
  'RcppArmadillo', 'RcppXPtrUtils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'shiny', 'DT'
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pcalg’
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)
> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFactor', 'BayesFM', 'blme', 'brms', 'cAIC4',
  'car', 'cgam', 'cplm', 'dbscan', 'drc', 'EGAnet', 'epiR', 'estimatr',
  'factoextra', 'FactoMineR', 'faraway', 'fixest', 'glmmTMB',
  'glmtoolbox', 'gt', 'ivreg', 'lme4', 'lmerTest', 'logistf', 'M3C',
  'marginaleffects', 'MCMCglmm', 'mediation', 'merDeriv', 'metaBMA',
  'mice', 'mmrm', 'nestedLogit', 'openxlsx', 'panelr', 'pbkrtest',
  'plm', 'PMCMRplus', 'PROreg', 'RcppEigen', 'rstan', 'rstanarm',
  'survey', 'svylme', 'TMB', 'WRS2'
Running examples in ‘parameters-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: p_direction.lm
> ### Title: Probability of Direction (pd)
> ### Aliases: p_direction.lm
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("bayestestR") && require("see", quietly = TRUE) && requireNamespace("sandwich")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ data(qol_cancer)
+ model <- lm(QoL ~ time + age + education, data = qol_cancer)
+ p_direction(model)
+ 
+ # based on heteroscedasticity-robust standard errors
+ p_direction(model, vcov = "HC3")
+ 
+ result <- p_direction(model)
+ plot(result)
+ ## Don't show: 
+ }) # examplesIf
> data(qol_cancer)
> model <- lm(QoL ~ time + age + education, data = qol_cancer)
> p_direction(model)
Probability of Direction (null: 0)

Parameter     |         95% CI |     pd
---------------------------------------
(Intercept)   | [58.46, 69.28] |   100%
time          | [-1.07,  2.85] | 81.29%
age           | [-0.32,  0.37] | 55.15%
educationmid  | [ 4.43, 13.09] | 99.99%
educationhigh | [ 9.33, 19.38] |   100%
> p_direction(model, vcov = "HC3")
Probability of Direction (null: 0)

Parameter     |         95% CI |     pd
---------------------------------------
(Intercept)   | [58.33, 69.41] |   100%
time          | [-1.13,  2.90] | 80.57%
age           | [-0.33,  0.38] | 55.99%
educationmid  | [ 4.21, 13.31] | 99.99%
educationhigh | [ 9.37, 19.34] |   100%
> result <- p_direction(model)
> plot(result)
Error: Package `ggridges` required for this function to work.
  Please install it by running `install.packages("ggridges")`.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'shinydashboard', 'TIMP', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'interp', 'GGally', 'lhs', 'plyr', 'reshape2'
checkRd: (-1) getParamNr.Rd:15: Lost braces
    15 | Default is code{FALSE}.}
       |                ^
checkRd: (-1) getRequirements.Rd:16: Lost braces
    16 | code{TRUE}.}
       |     ^
checkRd: (-1) sampleValue.Rd:15: Lost braces; missing escapes or markup?
    15 | Default is code {FALSE}.}
       |                 ^
checkRd: (-1) sampleValues.Rd:18: Lost braces; missing escapes or markup?
    18 | Default is code {FALSE}.}
       |                 ^
Running examples in ‘ParamHelpers-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generateDesign
> ### Title: Generates a statistical design for a parameter set.
> ### Aliases: generateDesign
> 
> ### ** Examples
> 
> ps = makeParamSet(
+   makeNumericParam("x1", lower = -2, upper = 1),
+   makeIntegerParam("x2", lower = 10, upper = 20)
+ )
> # random latin hypercube design with 5 samples:
> generateDesign(5, ps)
Error in requirePackages("lhs", why = "generateDesign", default.method = "load") : 
  For generateDesign please install the following packages: lhs
Calls: generateDesign -> requirePackages -> stopf
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppTOML’

Package suggested but not available for checking: ‘openxlsx’

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: 'dbscan', 'lhs', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘easyalluvial’

Packages suggested but not available for checking:
  'spelling', 'plotly', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) returns.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{...}{Other options including {type} which refers to the
       |                                      ^
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) PPS.fit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forbes400.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forbes400.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:11: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'gstat', 'leaflet', 'leafsync', 'sf', 'shiny', 'shinycssloaders',
  'stars'

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', 'RNifti', 'plyr', 'ARIbrain', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ast2ast', 'dfdr', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fst’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘netrankr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RSelenium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reticulate’
Packages suggested but not available for checking:
  'C50', 'ggrepel', 'keras', 'prodlim', 'ranger', 'tensorflow'
Package suggested but not available for checking: ‘AER’
Running examples in ‘PartCensReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cens.SMN.PCR
> ### Title: Estimation and diagnostics for partially linear censored
> ###   regression models
> ### Aliases: Cens.SMN.PCR
> ### Keywords: package censored censoring diagnostic partial partially
> 
> ### ** Examples
> 
> dtawage = get(data(PSID1976,package = "AER"))
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: get -> data -> find.package
Execution halted
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Rcpp', 'RcppArmadillo', 'RcppEigen', 'RcppNumerical'

Packages suggested but not available for checking: 'AER', 'CDatanet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggraph’
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown

Quitting from lines 102-107 [unnamed-chunk-3] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'cubature', 'DescTools', 'flexsurv',
  'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'genieclust', 'ggcorrplot', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘regtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘AER’
Note: skipping ‘mob.Rnw’ due to unavailable dependencies: 'AER'
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ipred’
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: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'copBasic', 'GGally', 'plotly', 'Rcpp'

Package suggested but not available for checking: ‘faraway’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Package suggested but not available for checking: ‘plyr’
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(passt)
  > 
  > test_check("passt")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 8 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-simulation.R:21:1'): (code run outside of `test_that()`) ───────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'plyr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-simulation.R:21:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'glmmTMB', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'terra', 'sf'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘gt’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'corrr', 'metan'

Packages suggested but not available for checking:
  'car', 'devtools', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggraph', 'ggkegg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BART', 'metR', 'pryr', 'twang'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘anomalize’
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'survminer', 'caret', 'pROC', 'clusterProfiler'

Packages suggested but not available for checking: 'qpdf', 'spelling'

VignetteBuilder package required for checking but not installed: ‘qpdf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'odbc', 'spelling', 'DT', 'gt'
Packages required but not available: 'clinUtils', 'plyr', 'reshape2'

Packages suggested but not available for checking:
  'pander', 'shiny', 'pdftools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plyr’
Packages required but not available:
  'raster', 'sf', 'Morpho', 'imager', 'RNiftyReg', 'geomorph',
  'ClusterR'

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: 'repmis', 'SelectBoost', 'WGCNA'

Packages suggested but not available for checking:
  'animation', 'c060', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'magick', 'sf'

Packages suggested but not available for checking: 'alphashape3d', 'imager'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'paws.analytics', 'paws.application.integration', 'paws.common',
  'paws.compute', 'paws.cost.management', 'paws.customer.engagement',
  'paws.database', 'paws.developer.tools', 'paws.end.user.computing',
  'paws.machine.learning', 'paws.management', 'paws.networking',
  'paws.security.identity', 'paws.storage'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘paws.common’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rmisc', 'plyr', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Package required but not available: ‘ibd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ade4', 'ape', 'DDD', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘latticeExtra’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘leaflet’

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
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigutilsr', 'mmapcharr', 'Rcpp', 'RSpectra'

Packages suggested but not available for checking:
  'plotly', 'shiny', 'spelling', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'pander'

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: 'huge', 'dagitty'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) twoby2Calibrate.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:87-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:97-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:111-116: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘optmatch’
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'interp', 'gMOIP'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcds', 'interp'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'reshape2', 'RcppEigen', 'StanHeaders'

Packages suggested but not available for checking: 'shiny', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcalg', 'lme4', 'sommer'

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: 'bigstatsr', 'dcov', 'Rfast', 'Rfast2'

Package suggested but not available for checking: ‘bigreadr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘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: 'ape', 'mvSLOUCH', 'phangorn', 'yuima'

Packages suggested but not available for checking: 'geiger', 'distory'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'PCMBase', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

Packages suggested but not available for checking: 'ggtree', 'mvSLOUCH'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cubature', 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SYNCSA', 'ape', 'picante', 'phylobase', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) getPCRAData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:29: Lost braces in \itemize; meant \describe ?
Skipping checking math rendering: package 'V8' unavailable
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'pcutils', 'ggrepel', 'reshape2', 'ggpubr', 'ade4'

Packages suggested but not available for checking:
  'picante', 'ggpmisc', 'NST', 'Rtsne', 'mixOmics', 'geosphere',
  'phyloseq', 'phyloseqGraphTest', 'plotly', 'umap', 'tidytree',
  'ggtree', 'ggtreeExtra', 'ape', 'DESeq2', 'ALDEx2', 'MetaNet',
  'zetadiv', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'stplanr', 'sf', 'crul'

Packages suggested but not available for checking: 'leaflet', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sarima', 'PolynomF'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Packages suggested but not available for checking:
  'ggpubr', 'pagedown', 'PMCMRplus', 'ggspatial', 'sf', 'magick',
  'ggimage', 'ggpmisc', 'UpSetR', 'plotly', 'leaflet', 'relaimpo',
  'ggraph', 'ggrepel', 'treemap', 'voronoiTreemap', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Packages required but not available:
  'FactoMineR', 'lme4', 'extraDistr', 'car'

Packages suggested but not available for checking:
  'brms', 'flexsurv', 'cmdstanr', 'rstan', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'minqa', 'glmnet', 'plyr', 'RcppArmadillo'

Packages suggested but not available for checking: 'imager', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plm’

Packages suggested but not available for checking: 'car', 'pglm', 'splm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘PythonInR’
Packages required but not available: 'pdftools', 'tokenizers'

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', 'qpdf'

Package suggested but not available for checking: ‘tesseract’

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: ‘glmnet’

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:
  'adabag', 'C50', 'caret', 'Cubist', 'ipred', 'keras', 'ranger',
  'reticulate'
Package suggested but not available for checking: ‘spelling’
Package suggested but not available for checking: ‘reshape2’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plm', 'pglm', 'lme4', 'glmmTMB'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'ddalpha', 'RcppArmadillo'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) embedded.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) embedded.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) ensemble.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) ensemble.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) staged.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) staged.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggpubr', 'frailtypack'

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'leaflet', 'leaflet.extras', 'gganimate'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘pdxTrees-vignette.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/pdxTrees.Rcheck/vign_test/pdxTrees/vignettes/pdxTrees-vignette_files/figure-html/unnamed-chunk-4-1.png
1152x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 30736 bytes
Input file size = 30850 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 27276
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 27276

Output IDAT size = 27276 bytes (3460 bytes decrease)
Output file size = 27354 bytes (3496 bytes = 11.33% decrease)


Quitting from lines 87-90 [leaflet packages] (pdxTrees-vignette.Rmd)
Error: processing vignette 'pdxTrees-vignette.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building ‘pdxTrees-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘pdxTrees-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘pder’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'geosphere', 'stevemisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'prodlim', 'riskRegression'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qwraps2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘datasets.Rmd’ using rmarkdown

Quitting from lines 46-50 [setup] (datasets.Rmd)
Error: processing vignette 'datasets.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building ‘datasets.Rmd’

--- re-building ‘fss.Rmd’ using rmarkdown

Quitting from lines 38-45 [namespaces] (fss.Rmd)
Error: processing vignette 'fss.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building ‘fss.Rmd’

SUMMARY: processing the following files failed:
  ‘datasets.Rmd’ ‘fss.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking:
  'DT', 'ggpubr', 'qwraps2', 'shiny', 'shinyBS', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'latticeExtra', 'Rcpp'

Packages suggested but not available for checking:
  'car', 'fields', 'georob', 'gstat', 'SpatialTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘echarts4r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ibdsim2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘MCMCglmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ape’

Package suggested but not available for checking: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘treemap’
Error(s) in re-building vignettes:
  ...
--- re-building ‘download.Rmd’ using rmarkdown
--- finished re-building ‘download.Rmd’

--- re-building ‘examples.Rmd’ using rmarkdown
--- finished re-building ‘examples.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown

Quitting from lines 22-25 [setup] (intro.Rmd)
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'treemap'
--- failed re-building ‘intro.Rmd’

--- re-building ‘pell.Rmd’ using rmarkdown
--- finished re-building ‘pell.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'DT', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rstan', 'Rcpp', 'rstantools', 'shiny', 'RcppEigen', 'StanHeaders'

Package suggested but not available for checking: ‘mice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'loa', 'latticeExtra', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'penalized', 'clogitL1'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'riskRegression', 'survcomp'

Packages suggested but not available for checking: 'ptmixed', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'latticeExtra', 'pacotest'

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: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GJRM’

Packages suggested but not available for checking: 'cartography', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'glmnet', 'fixest', 'collapse', 'devtools', 'RcppEigen'

Package suggested but not available for checking: ‘reshape2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

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 checking math rendering: package 'V8' unavailable
Packages required but not available:
  'mcmcse', 'Rcpp', 'RcppArmadillo', 'RcppGSL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘penalized’
Package required but not available: ‘Rcpp’

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.
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: 'Peptides', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘spelling’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = FALSE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Packages suggested but not available for checking: 'devtools', 'reshape2'
Running ‘testthat.R’ [10s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Perc)
  > 
  > test_check("Perc")
  [ FAIL 2 | WARN 9 | SKIP 0 | PASS 58 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Converters.R:37:3'): outputs are of correct format for dyadicLongConverter ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'reshape2'
  Backtrace:
      ▆
   1. ├─Perc::dyadicLongConverter(testMatrix) at test-Converters.R:37:3
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-Converters.R:51:3'): outputs are correct ───────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'reshape2'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal_to_reference(...) at test-Converters.R:51:3
   2. │ └─testthat::expect_known_value(..., update = update)
   3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
   4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
   5. ├─Perc::dyadicLongConverter(testMatrix)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base (local) withOneRestart(expr, restarts[[1L]])
   9.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 9 | SKIP 0 | PASS 58 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Perc.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Perc.Rcheck/vign_test/Perc/vignettes/Perc_files/figure-html/unnamed-chunk-12-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18409 bytes
Input file size = 18511 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 13049
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 13049

Output IDAT size = 13049 bytes (5360 bytes decrease)
Output file size = 13127 bytes (5384 bytes = 29.09% decrease)

** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Perc.Rcheck/vign_test/Perc/vignettes/Perc_files/figure-html/unnamed-chunk-13-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18293 bytes
Input file size = 18395 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12855
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12855

Output IDAT size = 12855 bytes (5438 bytes decrease)
Output file size = 12933 bytes (5462 bytes = 29.69% decrease)


Quitting from lines 179-181 [unnamed-chunk-15] (Perc.Rmd)
Error: processing vignette 'Perc.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘Perc.Rmd’

SUMMARY: processing the following file failed:
  ‘Perc.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'mirt', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'plotly', 'ggpubr', 'RPESE'
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) Return.portfolio.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:110-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:114-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:119-122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:123-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:130-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Found the following HTML validation problems:
Return.Geltner.html:58:32 (Return.Geltner.Rd:27): Warning: trimming empty <code>
centeredmoments.html:24:32 (centeredmoments.Rd:37): Warning: trimming empty <code>
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking: 'devtools', 'DMwR'
checkRd: (-1) classificationMetrics.Rd:85: Lost braces; missing escapes or markup?
    85 |   will use some extra notation, namely: TP = #{p == + & t == +} ; FP =
       |                                               ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |    ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                              ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                                                       ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |          ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |                          ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFactor', 'bayesplot', 'bigutilsr', 'blavaan',
  'brms', 'car', 'cplm', 'dagitty', 'dbscan', 'DHARMa', 'estimatr',
  'fixest', 'flextable', 'forecast', 'ftExtra', 'gamm4', 'ggdag',
  'glmmTMB', 'ICS', 'ICSOutlier', 'ivreg', 'lme4', 'multimode',
  'nestedLogit', 'qqplotr', 'RcppEigen', 'rstanarm', 'rstantools',
  'survey'
Running examples in ‘performance-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_distribution
> ### Title: Classify the distribution of a model-family using machine
> ###   learning
> ### Aliases: check_distribution
> 
> ### ** Examples
> 
> ## Don't show: 
> if (require("lme4") && require("parameters") && require("randomForest")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ data(sleepstudy, package = "lme4")
+ model <<- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+ check_distribution(model)
+ ## Don't show: 
+ }) # examplesIf
Loading required package: lme4
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘lme4’
> ## End(Don't show)
> ## Don't show: 
> if (require("see") && require("patchwork") && require("randomForest")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ plot(check_distribution(model))
+ ## Don't show: 
+ }) # examplesIf
Loading required package: see
Loading required package: patchwork
Loading required package: randomForest
randomForest 4.7-1.2
Type rfNews() to see new features/changes/bug fixes.
> plot(check_distribution(model))
Error in eval(ei, envir) : object 'model' not found
Calls: <Anonymous> ... withVisible -> eval -> eval -> plot -> check_distribution
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shiny', 'bs4Dash', 'DT', 'fresh', 'shinyFeedback', 'shinyWidgets'

Packages suggested but not available for checking:
  'colourpicker', 'miniUI', 'openxlsx', 'shinyjs', 'spelling', 'waiter'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinydashboard', 'shinyBS', 'DT', 'fresh'

Packages suggested but not available for checking:
  'shinydashboardPlus', 'openxlsx', 'colourpicker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bs4Dash', 'DT', 'shiny', 'colourpicker', 'golem', 'plotly',
  'shinyjs', 'shinyWidgets'

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
Package required but not available: ‘ipred’

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: ‘freealg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
Package required but not available: ‘plyr’

Packages suggested but not available for checking:
  'buildmer', 'car', 'glmmTMB', 'lme4', 'permuco'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'miniUI', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'personalized', 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AICcmodavg', 'BTSPAS', 'plyr', 'reshape2', 'SPAS'

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
checkRd: (-1) read_PN.Rd:15: Lost braces
    15 | A code{\link{marked_petrinet}}
       |       ^
Package required but not available: ‘RSelenium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'caper', 'picante', 'ade4', 'FD', 'animation', 'phytools'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Rcpp', 'RcppEigen'
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown

Quitting from lines 181-182 [unnamed-chunk-7] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
could not find plugin 'Rcpp'
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: 'sf', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'Directional', 'DirStats', 'rotasym', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plm’

Package suggested but not available for checking: ‘car’

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', 'KrigInv', 'RcppArmadillo'

Package suggested but not available for checking: ‘anMC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SAM', 'energy', '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.
Packages suggested but not available for checking: 'wordcloud', 'pander'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'bigmemory', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'reshape2', 'RcppArmadillo'

Package suggested but not available for checking: ‘plm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘odbc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'animation', 'Rcpp'

Package suggested but not available for checking: ‘gsDesign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gsDesign’
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'Rcpp', 'rstan', 'rstantools', 'RcppEigen', 'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'factoextra', 'bipartite', 'smerc'

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:
  'apex', 'magick', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages suggested but not available for checking: 'gt', 'plyr'
Packages suggested but not available for checking:
  'devtools', 'DT', 'miniUI', 'spelling'
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking: 'devtools', 'spelling'
Packages required but not available: 'altair', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reshape2', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'plotly', 'zeitgebr', 'shiny', 'shinythemes', 'shinydashboard',
  'shinycssloaders', 'shinyFiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) phasePlaneAnalysis.Rd:84: Lost braces; missing escapes or markup?
    84 | identified {see (3) above}, if this point is a saddle then the manifolds are
       |            ^
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘test.pdf’
Packages required but not available:
  'adabag', 'C50', 'caret', 'glmnet', 'HDclassif', 'ipred', 'klaR',
  'themis'

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:
  'shiny', 'shinyBS', 'DT', 'golem', 'plotly', 'rintrojs',
  'shinycssloaders', 'shinydashboard', 'shinydashboardPlus'

Package suggested but not available for checking: ‘shinytest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘reshape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'daymetr', 'MODISTools'

Packages suggested but not available for checking:
  'shiny', 'shinydashboard', 'leaflet', 'plotly', 'DT'

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: 'shiny', 'fields', 'car'
Packages required but not available: 'plyr', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘terra’

Package suggested but not available for checking: ‘tidyterra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qs’
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phers)
  > 
  > test_check('phers')
  Error in `FUN()`:
  ! In path: "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/phers.Rcheck/tests/testthat/setup.R"
  Caused by error in `library()`:
  ! there is no package called 'qs'
  Backtrace:
       ▆
    1. ├─testthat::test_check("phers")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::library("qs") at tests/testthat/setup.R:3:1
   15. │                         └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))
   16. └─testthat (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(...)
  Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'glmnet', 'lme4', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DT', 'spelling'
Packages required but not available: 'tm', 'shiny', 'smallstuff'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'blme', 'FactoMineR', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'qwraps2', 'reticulate'
Error(s) in re-building vignettes:
  ...
--- re-building ‘phoenix.Rmd’ using rmarkdown

Quitting from lines 17-29 [setup] (phoenix.Rmd)
Error: processing vignette 'phoenix.Rmd' failed with diagnostics:
there is no package called 'qwraps2'
--- failed re-building ‘phoenix.Rmd’

SUMMARY: processing the following file failed:
  ‘phoenix.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'DT', 'lingtypology'
Package required but not available: ‘Rcpp’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Running examples in ‘phosphoricons-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: html_dependency_phosphor
> ### Title: HTML dependency for Phosphor Icons
> ### Aliases: html_dependency_phosphor
> 
> ### ** Examples
> 
> 
> library(shiny)
Error in library(shiny) : there is no package called ‘shiny’
Execution halted
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  'ggspectra', 'photobiologyWavebands'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'photobiology', 'anytime'

Packages suggested but not available for checking:
  'hyperSpec', 'pavo', 'fda.usc', 'ggspectra', 'photobiologyWavebands'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  'ggspectra', 'photobiologyWavebands', 'photobiologyLEDs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  'photobiologyWavebands', 'photobiologyLamps', 'ggspectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'photobiology', 'photobiologyWavebands'

Package suggested but not available for checking: ‘ggspectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

Package suggested but not available for checking: ‘lutz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  'photobiologyWavebands', 'ggspectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  'photobiologyWavebands', 'ggspectra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'units', 'gunit', 'tealeaves'

Package suggested but not available for checking: ‘brms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phylobase', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'geometry', 'raster', 'gdistance'
Running examples in ‘phylin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract.val
> ### Title: Extact pairwise values from a matrix in a specified order.
> ### Aliases: extract.val
> ### Keywords: variogram kriging
> 
> ### ** Examples
> 
> 
> data(vipers)
> data(d.gen)
> 
> # calculate midpoints
> mp <- midpoints(vipers[,1:2])
Error in midpoints(vipers[, 1:2]) : 
  Package 'geometry' is needed for Delaunay triangulation.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘phylin_tutorial.Snw’ using Sweave

Error: processing vignette 'phylin_tutorial.Snw' failed with diagnostics:
 chunk 31 (label = midpoints) 
Error in midpoints(vipers[, 1:2]) : 
  Package 'geometry' is needed for Delaunay triangulation.

--- failed re-building ‘phylin_tutorial.Snw’

--- re-building ‘resistance_tutorial.Snw’ using Sweave

Error: processing vignette 'resistance_tutorial.Snw' failed with diagnostics:
 chunk 7 (label = conductanceraster) 
Error in library(gdistance) : there is no package called ‘gdistance’

--- failed re-building ‘resistance_tutorial.Snw’

SUMMARY: processing the following files failed:
  ‘phylin_tutorial.Snw’ ‘resistance_tutorial.Snw’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'ade4', 'ape', 'Rcpp', 'rncl', 'RNeXML'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phylobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ape’
Packages required but not available:
  'ape', 'glmnet', 'plyr', 'Rcpp', 'RcppArmadillo'

Packages suggested but not available for checking: 'phytools', 'TreeSim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'phytools', 'Rcpp', 'rstan', 'rstantools', 'RcppEigen',
  'StanHeaders'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'ggraph', 'phylolm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'SESraster', 'terra'

Package suggested but not available for checking: ‘phylobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'phangorn', 'betapart', 'terra', 'predicts', 'smoothr'

Packages suggested but not available for checking: 'phyloseq', 'V8'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reshape2’
Running examples in ‘phylosamp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gendist_roc_format
> ### Title: Make ROC curve from sensitivity and specificity
> ### Aliases: gendist_roc_format
> 
> ### ** Examples
> 
> # ebola-like pathogen
> R <- 1.5
> mut_rate <- 1
> 
> # use simulated generation distributions
> data('genDistSim')
> mean_gens_pdf <- as.numeric(genDistSim[genDistSim$R == R, -(1:2)])
> 
> # get theoretical genetic distance dist based on mutation rate and generation parameters
> dists <- as.data.frame(gendist_distribution(mut_rate = mut_rate,
+                        mean_gens_pdf = mean_gens_pdf,
+                        max_link_gens = 1))
> 
> dists <- reshape2::melt(dists,
+                         id.vars = 'dist',
+                         variable.name = 'status',
+                         value.name = 'prob')
Error in loadNamespace(x) : there is no package called ‘reshape2’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘L1_FalseDiscoveryRate.Rmd’ using rmarkdown
--- finished re-building ‘L1_FalseDiscoveryRate.Rmd’

--- re-building ‘L2_SampleSize.Rmd’ using rmarkdown
--- finished re-building ‘L2_SampleSize.Rmd’

--- re-building ‘L3_SensitivitySpecificity.Rmd’ using rmarkdown
--- finished re-building ‘L3_SensitivitySpecificity.Rmd’

--- re-building ‘L4_IllustrativeExamples.Rmd’ using rmarkdown

Quitting from lines 24-77 [gen_dist_compare_ebov] (L4_IllustrativeExamples.Rmd)
Error: processing vignette 'L4_IllustrativeExamples.Rmd' failed with diagnostics:
there is no package called 'reshape2'
--- failed re-building ‘L4_IllustrativeExamples.Rmd’

--- re-building ‘V1_CoefficientDetectionBias.Rmd’ using rmarkdown
--- finished re-building ‘V1_CoefficientDetectionBias.Rmd’

--- re-building ‘V2_SampleSizeCrossSectional.Rmd’ using rmarkdown
--- finished re-building ‘V2_SampleSizeCrossSectional.Rmd’

--- re-building ‘V3_ProbCrossSectional.Rmd’ using rmarkdown
--- finished re-building ‘V3_ProbCrossSectional.Rmd’

--- re-building ‘V4_SampleSizePeriodic.Rmd’ using rmarkdown
--- finished re-building ‘V4_SampleSizePeriodic.Rmd’

--- re-building ‘V5_ProbDetectPeriodic.Rmd’ using rmarkdown
--- finished re-building ‘V5_ProbDetectPeriodic.Rmd’

--- re-building ‘V6_IllustrativeExample.Rmd’ using rmarkdown
--- finished re-building ‘V6_IllustrativeExample.Rmd’

SUMMARY: processing the following file failed:
  ‘L4_IllustrativeExamples.Rmd’

Error: Vignette re-building failed.
Execution halted
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'TMB', 'sem', 'ape', 'phylobase', 'phylopath', 'RcppEigen'

Packages suggested but not available for checking:
  'semPlot', 'TreeTools', 'Rphylopars', 'phylolm', 'fishtree', 'phyr',
  'phylosignal', 'adephylo'

Package which this enhances but not available for checking: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phyloseq', 'ggnetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'adephylo', 'ape', 'phylobase', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ape’
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'NHPoisson', 'phylobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'reshape2', 'Rfast', 'RSpectra', 'RcppEigen', 'Rcpp',
  'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ape', 'Rcpp', 'lme4', 'latticeExtra', 'RcppArmadillo'

Packages suggested but not available for checking:
  'pez', 'picante', 'INLA', 'MCMCglmm', 'logistf', 'phylolm', 'DHARMa',
  'rr2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'keras', 'reticulate'
checkRd: (-1) pa-internal.Rd:11: Lost braces
    11 | code{l2df}: convert list to data.frame
       |     ^
checkRd: (-1) pa-internal.Rd:14: Lost braces
    14 | code{convertTZ}: force a new timezone on datetime
       |     ^
checkRd: (-1) pa-internal.Rd:16: Lost braces
    16 | code{createTime}: create datetime variable
       |     ^
checkRd: (-1) pa-internal.Rd:18: Lost braces
    18 | code{addDayIndex}: create ID_day variable from timestamp
       |     ^
Package required but not available: ‘Rcpp’

Packages suggested but not available for checking: 'childsds', 'spelling'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phytools', 'ape'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bestNormalize', 'RcppML'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'phangorn'

Packages suggested but not available for checking: 'animation', 'geiger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
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: 'univariateML', 'COINr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'animation', 'gridpattern', 'magick', 'pdftools', 'rayrender',
  'rayvertex', 'readobj'
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'car', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggiraph', 'ggforce', 'plyr'

Packages suggested but not available for checking: 'spelling', 'ranger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'nanotime', 'units'
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pinnacle.API’
Packages suggested but not available for checking: 'devtools', 'sf'
Error(s) in re-building vignettes:
  ...
--- re-building ‘pinochet.Rmd’ using rmarkdown

Quitting from lines 86-100 [trend] (pinochet.Rmd)
Error: processing vignette 'pinochet.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building ‘pinochet.Rmd’

SUMMARY: processing the following file failed:
  ‘pinochet.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) pinp.Rd:60: Lost braces; missing escapes or markup?
    60 |   {current date}"}
       |   ^
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'paws.storage', 'qs', 'shiny'
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

Package suggested but not available for checking: ‘deaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shiny’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'miniUI', 'shiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppEigen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'bayesplot'

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 ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/spelling.R’ failed.
Complete output:
  > spelling::spell_check_test(vignettes = TRUE, error = identical(Sys.getenv("TRAVIS"), "true"))
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package suggested but not available for checking: ‘spelling’
Packages suggested but not available for checking:
  'listviewer', 'openxlsx', 'shiny'
Packages suggested but not available for checking: 'ggrepel', 'spelling'
Error(s) in re-building vignettes:
  ...
--- re-building ‘pixar_film_ratings.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/pixarfilms.Rcheck/vign_test/pixarfilms/vignettes/pixar_film_ratings_files/figure-html/unnamed-chunk-3-1.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 72868 bytes
Input file size = 73042 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 59040
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 59040

Output IDAT size = 59040 bytes (13828 bytes decrease)
Output file size = 59118 bytes (13924 bytes = 19.06% decrease)


Quitting from lines 85-100 [unnamed-chunk-4] (pixar_film_ratings.Rmd)
Error: processing vignette 'pixar_film_ratings.Rmd' failed with diagnostics:
there is no package called 'ggrepel'
--- failed re-building ‘pixar_film_ratings.Rmd’

SUMMARY: processing the following file failed:
  ‘pixar_film_ratings.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'shiny', 'miniUI'

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:
  'ggforce', 'shiny', 'shinyWidgets', 'shinyjs', 'units', 'DT',
  'shinyalert'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'shiny', 'shinythemes', 'shinydashboard'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcpp’
Package suggested but not available for checking: ‘spelling’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'asciicast', 'spelling'
checkRd: (-1) deps.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deps.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deps.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkgdepR-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkgdepR-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkgdepR-package.Rd:18: Lost braces in \itemize; meant \describe ?
Skipping vignette re-building
Packages suggested but not available for checking: 'gt', 'magick', 'quarto'

VignetteBuilder package required for checking but not installed: ‘quarto’
Running examples in ‘pkgdown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: test-tables
> ### Title: Test case: tables
> ### Aliases: test-tables
> ### Keywords: internal
> 
> ### ** Examples
> 
> gt::gt(head(mtcars))
Error in loadNamespace(x) : there is no package called ‘gt’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'ggnetwork', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcpp’
Running ‘testthat.R’ [43s/24s]
  Running ‘wipe.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgload)
  > 
  > # Needed so that install.packages works correctly
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("pkgload")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 18 | PASS 339 ]
  
  ══ Skipped tests (18) ══════════════════════════════════════════════════════════
  • "pkgload" %in% dev_packages() is not TRUE (1): 'test-shim.R:126:3'
  • On CRAN (14): 'test-depend.R:5:3', 'test-depend.R:15:3',
    'test-depend.R:43:3', 'test-help.R:57:3', 'test-help.R:117:3',
    'test-help.R:128:3', 'test-help.R:141:3', 'test-help.R:162:3',
    'test-load-hooks.R:155:3', 'test-load.R:44:3', 'test-namespace.R:140:3',
    'test-shim.R:59:3', 'test-shim.R:135:3', 'test-source.R:2:3'
  • httr cannot be loaded (1): 'test-depend.R:58:3'
  • lang %in% c("C", "C.UTF-8") is TRUE (2): 'test-po.R:4:3', 'test-po.R:16:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dll.R:108:3'): load_all() can compile and load DLLs linked to Rcpp ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Rcpp'
  Backtrace:
      ▆
   1. ├─pkgload::load_all("testDllRcpp", reset = TRUE, quiet = TRUE) at test-dll.R:108:3
   2. │ └─pkgbuild::compile_dll(path, quiet = quiet)
   3. │   └─pkgbuild:::update_registration(...)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 18 | PASS 339 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘devtools’
checkRd: (-1) write.pkgbib.Rd:44: Lost braces; missing escapes or markup?
    44 | The Old version of this function {write.bib} has now been integrated
       |                                  ^
Found the following HTML validation problems:
options.html:83:1 (options.Rd:36): Warning: trimming empty <dt>
Package suggested but not available for checking: ‘ggrepel’
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'shiny', 'shinyjs', 'shinyWidgets'
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'pander', 'pmxTools', 'spelling', 'units'
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: ‘httk’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'tinytiger', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CVXR', 'RSpectra'

Packages suggested but not available for checking:
  'BayesMallows', 'BradleyTerry2', 'PLMIX', 'StatRank', 'hyper2',
  'lbfgs'

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: ‘raster’

Packages suggested but not available for checking: 'shiny', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Carlson', 'CVXR'

Package suggested but not available for checking: ‘freegroup’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'terra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'caret', 'MESS', 'pROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RcppRoll’

Packages suggested but not available for checking:
  'reactablefmtr', 'shiny', 'DT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'webshot2'

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: ‘DT’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sf', 'units'

Packages suggested but not available for checking: 'spelling', 'minidown'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘plsRcox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ape', 'plotly', 'plyr', 'reshape2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) one_design.Rd:125-126: Lost braces
   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
Packages required but not available:
  'ggtree', 'plyr', 'reshape2', 'seqinr', 'Seurat', 'SeuratObject',
  'useful'

Packages suggested but not available for checking:
  'ape', 'fgsea', 'ggrepel', 'harmony', 'iNEXT', 'kmer', 'phangorn',
  'phytools', 'Rtsne', 'sf', 'slingshot', 'tidytree', 'umap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggtext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'keras', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘interp’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'sf', 'stars', 'terra', 'RcppArmadillo'

Packages suggested but not available for checking:
  'leafem', 'leaflet', 'mapedit', 'mapview'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'ggforce', 'ggrepel', 'UpSetR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcpp', 'ggmcmc', 'reshape2', 'rankdist', 'StatRank', 'PlackettLuce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigalgebra', 'bigmemory', 'biglasso', 'glmnet', 'Rcpp',
  'RcppArmadillo'

Packages suggested but not available for checking: 'bigsnpr', 'bigstatsr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘collapse’

Packages suggested but not available for checking:
  'AER', 'car', 'pder', 'fixest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'torch', 'RcppArmadillo'

Packages suggested but not available for checking: 'spelling', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘Rcpp’
'LazyData' is specified without a 'data' directory
Running examples in ‘plogr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plogr-package
> ### Title: plogr: The 'plog' C++ Logging Library
> ### Aliases: plogr plogr-package
> 
> ### ** Examples
> 
> plogr_demo <- Rcpp::cppFunction(depends = "plogr", '
+ // C++ code begin
+ #include <plogr.h>
+ 
+ RObject plogr_demo() {
+   plog::init_r(plog::info);
+   LOG_INFO << "shown";
+   LOG_DEBUG << "not shown";
+   plog::init_r("DEBUG");
+   LOG_DEBUG << "shown now";
+   return R_NilValue;
+ }
+ 
+ #include <Rcpp.h> // not necessary to use plogr
+ // C++ code end
+ '
+ )
Error in loadNamespace(x) : there is no package called ‘Rcpp’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
checkRd: (-1) delta2a.Rd:21: Lost braces; missing escapes or markup?
    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
checkRd: (-1) ordprob.mple.Rd:29: Lost braces
    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
Packages required but not available:
  'reshape2', 'pcutils', 'ggforce', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘arm’
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘ape’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gganimate', 'raster', 'rerddap', 'sf'

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.
checkRd: (-1) add_bars.Rd:15: Lost braces
    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |       ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
Package suggested but not available for checking: ‘mixtools’
'LazyData' is specified without a 'data' directory
Running examples in ‘plotGMM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_GMM
> ### Title: Plots Mixture Components from Gaussian Mixture Models
> ### Aliases: plot_GMM
> 
> ### ** Examples
> 
> set.seed(235)
> mixmdl <- mixtools::normalmixEM(faithful$waiting, k = 2)
Error in loadNamespace(x) : there is no package called ‘mixtools’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("plotGMM")
  *Attention*: `plotGMM` is no longer actively developed. Instead, use the expanded package, `plotmm`. Thanks!
  > 
  > test_check("plotGMM")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_plot_GMM.R:6:3'): plot_GMM catches input errors ────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'mixtools'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_plot_GMM.R:6:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_plot_GMM.R:14:5'): plot_GMM successfully plots ─────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'mixtools'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_plot_GMM.R:14:5
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'plyr', 'ggfittext', 'magick'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘plotly’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘promises’

Packages suggested but not available for checking:
  'GGally', 'shiny', 'shinytest', 'listviewer', 'sf', 'reticulate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Getting-Started.Rmd’ using rmarkdown

Quitting from lines 51-62 [unnamed-chunk-2] (Getting-Started.Rmd)
Error: processing vignette 'Getting-Started.Rmd' failed with diagnostics:
there is no package called 'mixtools'
--- failed re-building ‘Getting-Started.Rmd’

SUMMARY: processing the following file failed:
  ‘Getting-Started.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'C50', 'glmnet', 'glmnetUtils', 'pre'
Package required but not available: ‘reshape2’

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.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'shiny', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘httpuv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plyr', 'shiny', 'MplusAutomation', 'Rcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package suggested but not available for checking: ‘FactoMineR’
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'reshape2', 'plyr', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'hdi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mixOmics’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'FactoMineR', 'reshape'
Error(s) in re-building vignettes:
  ...
--- re-building ‘plspm_introduction.Rnw’ using knitr

Quitting from lines 308-327 [rus_pls_xloads_ggplot] (plspm_introduction.Rnw)
Error: processing vignette 'plspm_introduction.Rnw' failed with diagnostics:
there is no package called 'reshape'
--- failed re-building ‘plspm_introduction.Rnw’

SUMMARY: processing the following file failed:
  ‘plspm_introduction.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plsRglm’

Package suggested but not available for checking: ‘bipartite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'plsRglm', 'mixOmics', 'survcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bipartite', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
'LazyData' is specified without a 'data' directory
Packages required but not available: 'httpuv', 'promises'

Packages suggested but not available for checking:
  'later', 'spelling', 'geojsonsf', 'sf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plumber', 'httpuv', 'later', 'promises', 'urltools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plyr’
Package suggested but not available for checking: ‘gt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘comprehensive-affiliation-schema.Rmd’ using rmarkdown
--- finished re-building ‘comprehensive-affiliation-schema.Rmd’

--- re-building ‘plume-workflow.Rmd’ using rmarkdown
--- finished re-building ‘plume-workflow.Rmd’

--- re-building ‘plume.Rmd’ using rmarkdown

Quitting from lines 11-20 [unnamed-chunk-1] (plume.Rmd)
Error: processing vignette 'plume.Rmd' failed with diagnostics:
there is no package called 'gt'
--- failed re-building ‘plume.Rmd’

--- re-building ‘working-in-other-languages.Rmd’ using rmarkdown
--- finished re-building ‘working-in-other-languages.Rmd’

SUMMARY: processing the following file failed:
  ‘plume.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'fracture', 'nombre'
checkRd: (-1) plu_more.Rd:16: Lost braces; missing escapes or markup?
    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plu)
  > 
  > test_check("plu")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 271 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-is_capital.R:119:3', 'test-is_capital.R:160:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plu_more.R:106:3'): cardinal ───────────────────────────────────
  Error: Could not find the function `fn`
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-plu_more.R:106:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─plu::plu_more(letters, fn = nombre::cardinal)
    5.   └─plu::get_fun(fn)
    6.     └─base::tryCatch(...)
    7.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    8.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    9.           └─value[[3L]](cond)
   10.             └─plu:::error("Could not find the function ", code(fn_input))
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 271 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘baizer’

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: ‘tableone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clusterProfiler', 'glmnet', 'pROC', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'pcaMethods', 'RcppArmadillo'

Packages suggested but not available for checking:
  'DESeq2', 'plotly', 'pmartRdata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘BWStest’

Packages suggested but not available for checking: 'car', 'NSM3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
Packages required but not available: 'geiger', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘enviGCMS’

Packages suggested but not available for checking: 'shiny', 'MSnbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sf', 'Rcpp'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
Skipping checking math rendering: package 'V8' unavailable
Packages suggested but not available for checking:
  'caret', 'forecast', 'glmnet'
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rtdists', 'V8'
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available:
  'shinyBS', 'golem', 'rclipboard', 'shiny', 'shinyAce', 'shinyFiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘ggdist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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: 'Rfast', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Packages suggested but not available for checking:
  'convey', 'SIPDIBGE', 'srvyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Packages suggested but not available for checking:
  'convey', 'SIPDIBGE', 'srvyr'

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
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fuzzyjoin’

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:
  'lhs', 'raster', 'trend', 'gdistance', 'qs'

Package suggested but not available for checking: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'logistf', 'plyr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘gt’

Packages suggested but not available for checking: 'ggforce', 'odbc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sf', 'inlabru', 'terra', 'raster', 'blockCV'

Packages suggested but not available for checking:
  'INLA', 'rasterVis', 'ggmap', 'spocc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘spelling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rARPACK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plyr', 'TripleR', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) pois.fe.robust.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
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: ‘Rcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'Rcpp', 'RcppArmadillo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spelling’
Skipping checking math rendering: package 'V8' unavailable
Package required but not available: ‘shiny’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Skipping checking math rendering: package 'V8' unavailable
Packages required but not available: 'quanteda', 'spacyr', 'textstem'

Packages suggested but not available for checking:
  'tesseract', 'quanteda.textstats', 'keyATM', 'pdftools', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reshape2’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcpp', 'grf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'rstatix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.